bluuebunny/crossref_metadata_2025 huggingface dataset:
Transmembrane dynamics of water exchange in human brain
Authors: He Xiang , Raichle Marcus E. , Yablonskiy Dmitriy A.
Published: September 2011

Tracking arterial spin labeled (ASL) water in the human brain with magnetic resonance imaging can provide important information on the dynamics of the trans‐capillary and trans‐membrane water exchange. This information however, is not only important from a basic biological standpoint, but also is essential for deciphering positron emission tomography and MRI perfusion experiments based on the movement of labeled water. While substantial information exists on water exchange through cellular membranes in vitro, the in vivo information remains limited and controversial. In this MRI study, we use a combination of pulsed ASL and recently developed quantitative blood‐oxygen‐level‐dependent technique to address this question. Our approach is based on the measurements of the intrinsic MR transverse relaxation (T) properties of the ASL‐labeled water. We discovered that T of the ASL‐labeled water in the extravascular space is 87 ms ± 10 ms while T of the corresponding tissue water is much shorter, 50 ms ± 4 ms. This suggests that the ASL‐labeled water does not reach equilibrium with the extravascular tissue and is mostly localized to the extraneuronal space. We estimated that the water transport time through the neuronal membranes is on the order of several tens of seconds; a finding consistent with older PET tracer kinetic studies using 15O‐water. Magn Reson Med, 2012. © 2011 Wiley Periodicals, Inc.
DCE and DW MRI in monitoring response to androgen deprivation therapy in patients with prostate cancer: A feasibility study
Authors: Barrett T. , Gill A. B. , Kataoka M. Y. , Priest A. N. , Joubert I. , McLean M. A. , Graves M. J. , Stearn S. , Lomas D. J. , Griffiths J. R. , Neal D. , Gnanapragasam V. J. , Sala E.
Published: September 2011

Androgen deprivation therapy (ADT) is a key primary treatment for advanced and metastatic prostate cancer and is an important neoadjuvant before radiotherapy. We evaluated 3.0 T dynamic contrast‐enhanced MRI and diffusion‐weighted (DW) MRI in monitoring ADT response. Twenty‐three consecutive patients with prostate cancer treated by primary ADT were included. Imaging was performed at baseline and 3 months posttreatment with ADT. After 3 months therapy there was a significant reduction in all dynamic contrast‐enhanced MRI parameters measured in tumor regions of interest (Ktrans, kep, vp, IAUGC‐90); P < 0.001. Areas of normal‐appearing peripheral zone showed no significant change; P = 0.285–0.879. Post‐ADT, there was no significant change in apparent diffusion coefficient values in tumors, whilst apparent diffusion coefficient values significantly decreased in areas of normal‐appearing peripheral zone, from 1.786 × 10−3 mm2/s to 1.561 × 10−3 mm2/s; P = 0.007. As expected the median Prostate‐Specific Antigen (PSA) significantly reduced from 30 ng/mL to 1.5 ng/mL posttreatment, and median prostate volume dropped from 47.6 cm3 to 24.9 cm3; P < 0.001. These results suggest that dynamic contrast‐enhanced MRI and diffusion‐weighted MRI offer different information but that both could prove useful adjuncts to the anatomical information provided by T2‐weighted imaging. dynamic contrast‐enhanced as a marker of angiogenesis may help demonstrate ADT resistance and diffusion‐weighted imaging may be more accurate in determining presence of tumor cell death versus residual tumor. Magn Reson Med, 2012. © 2011 Wiley Periodicals, Inc.
Sparsity and low‐contrast object detectability
Authors: Trzasko Joshua D. , Bao Zhonghao , Manduca Armando , McGee Kiaran P. , Bernstein Matt A.
Published: September 2011

The application of sparsity‐driven reconstruction methods to MRI to date has largely focused on situations where high‐contrast features (e.g., gadolinium‐enhanced vessels) are of primary interest. In clinical practice, however, low contrast features such as subtle lesions are often of equal or greater interest. Using an American College of Radiology MR quality assurance phantom and test, we describe a novel framework for systematically and automatically evaluating the low‐contrast object detectability performance of different undersampled image reconstruction methods. This platform is used to evaluate three such methods, two based on classic Tikhonov regularization and one sparsity‐driven method based on ℓ1‐norm minimization (which is commonly used in compressive sensing, also known as compressed sensing, applications), across a wide range of sampling rates and parameterizations. Both the automated evaluation system and a manual evaluation of anatomical images with numerically‐generated low contrast inserts demonstrate that sparse reconstructions exhibit superior low‐contrast object detectability performance compared to both Tikhonov‐regularized reconstructions. The implications of this result, and potential applications of both the described low‐contrast object detectability platform and generalizations of it are then discussed. Magn Reson Med, 2011. © 2011 Wiley‐Liss, Inc.
Generalized spatiotemporal myocardial strain analysis for DENSE and SPAMM imaging
Authors: Young Alistair A. , Li Bo , Kirton Robert S. , Cowan Brett R.
Published: September 2011

Displacement encoding using stimulated echoes (DENSE) and spatial modulation of magnetization (SPAMM) are MRI techniques for quantifying myocardial displacement and strain. However, DENSE has not been compared against SPAMM in phantoms exhibiting nonhomogeneous strain, and interobserver variability has not been compared between DENSE and SPAMM. To perform these comparisons, there is a need for a generalized analysis framework for the evaluation of myocardial strain. A spatiotemporal mathematical model was used to represent myocardial geometry and motion. The model was warped to each frame using tissue displacement maps calculated from either automated phase unwrapping (DENSE) or nonrigid registration (SPAMM). Strain and motion were then calculated from the model using standard methods. DENSE and SPAMM results were compared in a deformable gel phantom exhibiting known nonhomogeneous strain, and interobserver errors were determined in 19 healthy human volunteers. Nonhomogeneous strain in the phantom was accurately quantified using both DENSE and SPAMM. In the healthy volunteers, DENSE produced better interobserver errors than SPAMM for radial strain (−0.009 ± 0.069 vs. 0.029 ± 0.152, respectively, bias ±95% confidence interval). In conclusion, generalized spatiotemporal modeling enables robust myocardial strain analysis for DENSE or SPAMM. Magn Reson Med, 2011. © 2011 Wiley‐Liss, Inc.
Subject‐specific estimation of respiratory navigator tracking factor for free‐breathing cardiovascular MR
Authors: Moghari Mehdi H. , Hu Peng , Kissinger Kraig V. , Goddu Beth , Goepfert Lois , Ngo Long , Manning Warren J. , Nezafat Reza
Published: September 2011

A mean respiratory navigator tracking factor of 0.6 is commonly used to estimate the respiratory motion of the heart from the displacement of the right hemi‐diaphragm. A constant tracking factor can generate significant residual error in estimation of the respiratory motion of the heart for the cases where the actual tracking factor highly deviates from 0.6. In this study, we implemented and evaluated a robust method to calculate a subject‐specific tracking factor for free‐breathing high resolution cardiac MR. The subject‐specific tracking factor was calculated from two consecutive navigator signals placed on the right hemi‐diaphragm and the basal left ventricle in a training phase. To verify the accuracy of the estimated subject‐specific tracking factor, nineteen subjects were recruited for comparing the estimated tracking factor in real‐time with an image‐based tracking factor, calculated off‐line. Subsequently, in seven adult subjects, whole‐heart or targeted coronary artery MR images were acquired using the estimated subject‐specific tracking factor and visually compared with those acquired using a constant (0.6) tracking factor. It was shown that the proposed method can accurately estimate the subject‐specific tracking factor and improve the quality of coronary images when the subject‐specific tracking factor differs from 0.6. Magn Reson Med, 2011. © 2011 Wiley‐Liss, Inc.
Discrimination of spinal and bulbar muscular atrophy from amyotrophic lateral sclerosis using sensory nerve action potentials
Authors: Hama Tetsuo , Hirayama Masaaki , Hara Takashi , Nakamura Tomohiko , Atsuta Naoki , Banno Haruhiko , Suzuki Keisuke , Katsuno Masahisa , Tanaka Fumiaki , Sobue Gen
Published: September 2011

Introduction:

Spinal and bulbar muscular atrophy (SBMA) and amyotrophic lateral sclerosis (ALS) are motor neuron diseases. Sensory impairment is sometimes observed, and electrophysiological involvement has been described in the sensory nerves of SBMA patients. We hypothesized that a sensory nerve conduction study (NCS) could be used to discriminate SBMA from ALS.

Methods:

We compared the results from NCSs in a total of 120 SBMA cases confirmed by genetic analysis, 188 ALS cases, and 50 normal subjects.

Results:

Sensory nerve action potential (SNAP) amplitudes of the SBMA group were significantly lower than in the ALS and control groups. In addition, receiver‐operating characteristic curve analysis for SNAP amplitude showed that a cut‐off value of 13.8 μV for median, 10.7 μV for ulnar, and 9.9 μV for sural nerve best discriminated SBMA from ALS.

Conclusions:

The specific decrease of SNAP amplitude in SBMA provides another useful tool for the differential diagnosis of motor neuron diseases. Muscle Nerve, 2012
Relapsed acute myelogenous leukemia of brachial plexus after marrow transplant
Authors: Sweet Jennifer A. , Jones Robert V. , Siu Alan , DePalma Louis , Caputy Anthony J.
Published: September 2011

We present a detailed description of brachial plexus infiltration by acute myelogenous leukemia (AML) in the setting of a remission bone marrow biopsy, without evidence of leukemia by flow cytometric analysis. This case illustrates the possibility of dormant leukemic cells in the peripheral nervous system (PNS) in a patient in apparent clinical remission. In patients with an unexplained brachial plexopathy and a history of AML, leukemic infiltrate of the PNS must be considered. Muscle Nerve, 2012
Variational multiscale enrichment for modeling coupled mechano‐diffusion problems
Authors: Oskay Caglar
Published: September 2011

In this paper, a new multiscale–multiphysics computational methodology is devised for the analysis of coupled diffusion–deformation problems. The proposed methodology is based on the variational multiscale principles. The basic premise of the approach is accurate fine‐scale representation at a small subdomain where it is known a priori that important physical phenomena are likely to occur. The response within the remainder of the problem domain is idealized on the basis of coarse‐scale representation. We apply this idea to evaluate a coupled mechano‐diffusion problem that idealizes the response of titanium structures subjected to a thermo–chemo–mechanical environment. The proposed methodology is used to devise a multiscale model in which the transport of oxygen into titanium is modeled as a diffusion process, whereas the mechanical response is idealized using concentration‐dependent elasticity equations. A coupled solution strategy based on operator split is formulated to evaluate the coupled multiphysics and multiscale problem. Numerical experiments are conducted to assess the accuracy and computational performance of the proposed methodology. Numerical simulations indicate that the variational multiscale enrichment has reasonable accuracy and is computationally efficient in modeling the coupled mechano‐diffusion response. Copyright © 2011 John Wiley & Sons, Ltd.
Superconvergence analysis for time‐dependent Maxwell's equations in metamaterials
Authors: Huang Yunqing , Li Jichun , Lin Qun
Published: September 2011

In this article, we consider the time‐dependent Maxwell's equations modeling wave propagation in metamaterials. One‐order higher global superclose results in the L2 norm are proved for several semidiscrete and fully discrete schemes developed for solving this model using nonuniform cubic and rectangular edge elements. Furthermore, L∞ superconvergence at element centers is proved for the lowest order rectangular edge element. To our best knowledge, such pointwise superconvergence result and its proof are original, and we are unaware of any other publications on this issue. © 2011 Wiley Periodicals, Inc. Numer Methods Partial Differential 2011
Correlates of stages of change for physical activity in adults with multiple sclerosis
Authors: Plow Matthew A. , Finlayson Marcia , Cho Chi
Published: September 2011

The Transtheoretical Model (TTM) is commonly used to understand physical activity (PA) behavior in the general population; however, few researchers have explored its relevance for persons with multiple sclerosis (MS). We examined the relative importance of health (symptoms and mobility impairments) and TTM constructs (behavioral and cognitive processes of change) in influencing stages of change placement for PA in a sample of 303 persons with MS using discriminant function analysis. The overall accuracy of predicting stages of change was 58.75%. Behavioral (r2 = .35) and cognitive processes (r2 = .17) accounted for the most variance, followed by mobility (r2 = .11) and self‐efficacy (r2 = .05). Results provide support for evaluating whether TTM‐based interventions can promote PA in adults with MS. © 2011 Wiley Periodicals, Inc. Res Nurs Health 34:378–388, 2011
Graphene nanocomposites based on poly(vinylidene fluoride): Structure and properties
Authors: Yu Jinhong , Jiang Pingkai , Wu Chao , Wang Lichun , Wu Xinfeng
Published: September 2011

A nanocomposite of Poly(vinylidene fluoride) (PVDF) was prepared with graphene sheets (GSs), which are a novel filler by a solution method. The structure‐properties relationships of PVDF/GSs nanocomposites were studied. The results of differential scanning calorimetry and X‐ray diffraction show that addition of GSs to the PVDF matrix promotes an α phase to β phase transformation of the polymer crystal. The nanocomposites exhibit significant increases in dynamic mechanical properties and thermal stability compared to the neat PVDF. In addition, the incorporation of GSs in PVDF indicated excellent optical transparency at the lowest weight fractions of GSs and modified wettability of PVDF. POLYM. COMPOS., 2011. © 2011 Society of Plastics Engineers
Toughening effect of cellulose nanowhiskers on polyvinyl acetate: Fracture toughness and viscoelastic analysis
Authors: Gong Guan , Mathew Aji P. , Oksman Kristiina
Published: September 2011

The toughening effect of cellulose nanowhiskers (CNWs) on modified polyvinyl acetate (PVAc) was analyzed with the help of morphology, relaxation, and creep behavior. The CNWs together with bound moisture at the matrix/whisker interfaces resulted in significant improvement in resistance to crack initiation and propagation. The magnitude of plastic deformation of the nanocomposites was higher than that of the neat PVAc. The relaxation temperature decreased, while the width of the damping peak increased with increasing CNW and moisture contents. The results from creep modeling showed that the instantaneous elastic modulus first increased and then decreased with the addition of CNWs, while the time‐dependent elasticity and viscosity decreased. The results suggested that the reinforcing effect of the CNWs was overwhelmed by the plasticizing effect of the bound moisture. Furthermore, low concentrations of CNWs significantly improved the fracture toughness of PVAc at the minor cost of strength, stiffness, and creep resistance. In this article, we present a novel approach to studying the toughening effect of CNWs on polymers using fracture tests and viscoelastic modeling. POLYM. COMPOS., 2011. © 2011 Society of Plastics Engineers
Centrifugal partition chromatography in the separation of natural products
Authors: Marston A. , Slacanin I. , Hostettmann K.
Published: September 2011

Recent innovations in liquid/liquid chromatographic techniques have led to a resurgence of interest in their use for the separation of natural products. Commercially available instruments which rely on centrifugal acceleration to speed up separation times are based either on a battery of cartridges or on a rotating multilayer coil and can be employed either as analytical tools or for preparative purposes. While solvent consumption is low, milligram to gram quantities are capable of being separated. Aqueous and non‐aqueous two‐phase solvent systems are compatible with these techniques and numerous applications involving simple and complex mixtures of natural products, both polar and non‐polar, have been demonstrated.
Quantitative glucosinolate analysis in Brassica seeds by X‐ray fluorescence spectroscopy
Authors: Schnug E. , Haneklaus S.
Published: September 2011

X‐ray fluorescence spectroscopy (X‐RF) is an indirect method which is suitable for the quantification of the total glucosinolate content of Brassica seeds. The X‐RF method is based on two major principles: the close relationship between total sulphur and total glucosinolate content in rapeseed and the distinctive applicabilities of X‐ray fluorescence spectroscopy for total sulphur determination in organic matter. The whole preparation procedure consists of only three steps and needs less than five minutes per sample. A special advantage of the method is the availability of a centralized calibration system which ensures the comparability of data derived from different laboratories.
Modeling the continuous entrapment and growth of gas bubbles during bulk polymerization of methyl methacrylate
Authors: Sahni Hitesh , Gupta Santosh K. , Mehra Anurag
Published: September 2011

Gas bubbles get entrapped continuously during bulk polymerization in stirred batch reactors. Once entrapped, these cannot escape because of the increasing viscosity of the reaction mass. The bubbles also grow with time due to the diffusion of the monomer. This phenomenon is modeled using an Eulerian‐Lagrangian population‐balance approach along with the equations describing the kinetics of polymerization. It is assumed that there is no nucleation of bubbles. An empirical rate of entrapment, Rentrap,i(viscosity, bubble diameter) is assumed for the polymerization of methyl methacrylate (MMA), an example system. The model parameters are tuned using experimental data on this system under near‐isothermal conditions in a 1‐L, fully instrumented stainless steel reactor with an anchor agitator. The model predictions are found to be in reasonable accord with experimental data under different conditions of polymerization. The study of this phenomenon has important design implications since the pre‐polymerization stage ends as soon as stable clusters of bubbles get formed. Further polymerization is normally carried out in tubular reactors or in molds. POLYM. ENG. SCI., 2011. © 2011 Society of Plastics Engineers
Protein modulation in mouse heart under acute and chronic hypoxia
Authors: Viganò Agnese , Vasso Michele , Caretti Anna , Bravatà Valentina , Terraneo Laura , Fania Chiara , Capitanio Daniele , Samaja Michele , Gelfi Cecilia
Published: September 2011

Exploring cellular mechanisms underlying beneficial and detrimental responses to hypoxia represents the object of the present study. Signaling molecules controlling adaptation to hypoxia (HIF‐1α), energy balance (AMPK), mitochondrial biogenesis (PGC‐1α), autophagic/apoptotic processes regulation and proteomic dysregulation were assessed. Responses to acute hypoxia (AH) and chronic hypoxia (CH) in mouse heart proteome were detected by 2‐D DIGE, mass spectrometry and antigen–antibody reactions. Both in AH and CH, the results indicated a deregulation of proteins related to sarcomere stabilization and muscle contraction. Neither in AH nor in CH the HIF‐1α stabilization was observed. In AH, the metabolic adaptation to lack of oxygen was controlled by AMPK activation and sustained by an up‐regulation of adenosylhomocysteinase and acetyl‐CoA synthetase. AH was characterized by the mitophagic protein Bnip 3 increment. PGC‐1α, a master regulator of mitochondrial biogenesis, was down‐regulated. CH was characterized by the up‐regulation of enzymes involved in antioxidant defense, in aldehyde bio‐product detoxification and in misfolded protein degradation. In addition, a general down‐regulation of enzymes controlling anaerobic metabolism was observed. After 10 days of hypoxia, cardioprotective molecules were substantially decreased whereas pro‐apoptotic molecules increased accompained by down‐regulation of specific target proteins.
Feature‐based classification of native and non‐native protein–protein interactions: Comparing supervised and semi‐supervised learning approaches
Authors: Zhao Nan , Pang Bin , Shyu Chi‐Ren , Korkin Dmitry
Published: September 2011

Structural knowledge about protein–protein interactions can provide insights to the basic processes underlying cell function. Recent progress in experimental and computational structural biology has led to a rapid growth of experimentally resolved structures and computationally determined near‐native models of protein–protein interactions. However, determining whether a protein–protein interaction is physiological or it is the artifact of an experimental or computational method remains a challenging problem. In this work, we have addressed two related problems. The first problem is distinguishing between the experimentally obtained physiological and crystal‐packing protein–protein interactions. The second problem is concerned with the classification of near‐native and inaccurate docking models. We first defined a universal set of interface features and employed a support vector machines (SVM)‐based approach to classify the interactions for both problems, with the accuracy, precision, and recall for the first problem classifier reaching 93%. To improve the classification, we next developed a semi‐supervised learning approach for the second problem, using transductive SVM (TSVM). We applied both classifiers to a commonly used protein docking benchmark of 124 complexes. We found that while we reached the classification accuracies of 78.9% for the SVM classifier and 80.3% for the TSVM classifier, improving protein‐docking methods by model re‐ranking remains a challenging problem.
Experimental and theoretical studies on the one‐photon and two‐photon properties of a series of carbazole derivatives containing styrene
Authors: Li Liang , Wu Yiqun , Zhou Qinling , He Chunying
Published: September 2011

Symmetric‐type carbazole derivatives show great potential for application in two‐photon absorption (TPA) materials and organic light‐emitting diodes. The absorption spectra and fluorescence emission spectra of three different N‐alkyl symmetric‐type carbazole derivatives were investigated. The density functional theory (DFT) time‐dependent‐DFT//Becke, three‐parameter, Lee–Yang–Parr/6‐31 G* method has been used to theoretically study one‐photon absorption properties. The computational results are in good agreement with the available experimental values. The two‐photon excited fluorescence of the compounds was surveyed by 120 fs pulse at 790 nm Ti: sapphire laser operating at 1 kHz repetition rate. Two‐photon excited fluorescence was obtained in the range of 380–600 nm, and TPA cross‐sections were calculated. The TPA properties of the series of compounds were investigated by the ZINDO/single and double electronic excitation configuration interaction method. The influence of the chemical structure of the compounds on two‐photon optical properties was discussed. The results show how the different changes in one‐photon absorption and TPA properties on the basis of lengthening the conjugated bridge and the different carbazole N‐alkyl substituents are attributed to the transition dipole moment in the excited process. Copyright © 2011 John Wiley & Sons, Ltd.
Soluble, redox‐active, and blue‐emitting poly(amide‐hydrazide)s and poly(amide‐1,3,4‐oxadiazole)s containing pyrenylamine units
Authors: Kung Yi‐Chun , Hsiao Sheng‐Huei
Published: September 2011

Two new aromatic poly(amide‐hydrazide)s (PAHs)‐bearing electroactive pyrenylamine units in the backbone were prepared from the phosphorylation polycondensation reactions of N,N‐di(4‐carboxyphenyl)‐1‐aminopyrene (1) with p‐aminobenzoyl hydrazide (p‐ABH) and m‐aminobenzoyl hydrazide (m‐ABH), respectively. The PAHs could be further cyclodehydrated into the corresponding poly(amide‐1,3,4‐oxadiazole)s in the range of 300–400 °C in the solid film state. All the hydrazide and oxadiazole polymers were soluble in many polar organic solvents and could afford flexible and strong films via solution casting. The poly(amide‐1,3,4‐oxdiazole)s had high glass‐transition temperatures (294–309 °C) and high thermal stability (10% weight‐loss temperature in excess of 520 °C). The dilute solutions of all the hydrazide and oxadiazole polymers showed strong fluorescence with emission maxima around 457–459 nm in the blue region. Copolymers obtained from the polycondensation of equimolar mixture of diacid 1 and 4,4′‐oxydibenzoic acid with p‐ABH or m‐ABH exhibited a significantly increased fluorescence quantum efficiency in comparison with the homopolymers. Cyclic voltammetry results indicated that all the hydrazide and oxadiazole polymers exhibited an ambipolar (n‐ and p‐doping processes) and electrochromic behavior. © 2011 Wiley Periodicals, Inc. J Polym Sci Part A: Polym Chem, 2011.
Theoretical perspective on properties of DNA‐functionalized surfaces
Authors: Singh Abhishek , Eksiri Hamed , Yingling Yaroslava G.
Published: September 2011

The molecular recognition properties of DNA gave rise to many novel materials and applications such as DNA biosensors, DNA‐functionalized colloidal materials, DNA origami and DNA‐based directed surface assembly. The DNA‐functionalized surfaces are used in biosensors and for programmed self‐assembly of biological, organic and inorganic moieties into novel materials. However, surface density, length, and linker design of the surface functionalized DNAs significantly influence the properties of DNA‐driven assemblies and materials. This perspective discusses the understanding of structure and dynamics of DNA immobilized on the surfaces from the theoretical point of view including recent progress in analytical theories, atomistic simulations, and coarse‐grained models. © 2011 Wiley Periodicals, Inc. J Polym Sci Part B: Polym Phys 49: 1563–1568, 2011
Interdisciplinary therapy improves biomarkers profile and lung function in asthmatic obese adolescents
Authors: da Silva Patrícia Leão , de Mello Marco Túlio , Cheik Nadia Carla , Sanches Priscila Lima , Correia Fabíola Alvise , de Piano Aline , Corgosinho Flávia Campos , da Silveira Campos Raquel Munhoz , do Nascimento Claudia M.O. , Oyama Lila M. , Tock Lian , Tufik Sérgio , Dâmaso Ana R.
Published: September 2011

Background

The simultaneous rise in the prevalence of asthma and obesity in the world, have demonstrated the importance of the development of treatment strategies. The purpose of this study was to evaluate the short‐ and long‐term results of interdisciplinary therapy on inflammatory biomarkers and lung function in asthmatics obese adolescents.

Methods

Seventy‐six post‐pubertal obese adolescents were recruited, including 50 non‐asthmatics [body mass index (BMI), 36 ± 5 kg/m2) and 26 asthmatics (BMI, 39 ± 4 kg/m2). Body composition was measured by plethysmography, and visceral fat was analyzed by ultrasound. Serum levels of adiponectin, leptin, and C‐reactive protein (CRP) were analyzed. Asthma and lung function were evaluated according to the American Thoracic Society criteria. Patients were submitted to 1‐year weight loss interdisciplinary intervention consisting of medical, nutritional, exercise, and psychological therapy.

Results

After interdisciplinary intervention, the lung function and pro/anti‐inflammatory adipokines improved significantly in both groups. Most importantly, there was an increase in adiponectin [4 (1.86–12.9) to 5.1 (2.48–16)], a reduction in CRP [2,073 (385–9,174) to 1,538 (205–7,083)] and leptin concentrations [59 (29–69) to 33 (9–49)] in the asthmatics patients. Furthermore, it was observed a reduction in asthma severity after treatment. In addition, Δ adiponectin was an independent factor to improve lung function after therapy in both groups.

Conclusions

Interdisciplinary therapy resulted in beneficial changes in inflammatory biomarkers profile and lung function in asthmatic and non‐asthmatic obese adolescents. Additionally, for the first time we showed that change in adiponectin level was an independent predictor to improve lung function in Brazilian obese adolescents. Pediatr Pulmonol. 2012; 47:8–17. © 2010 Wiley Periodicals, Inc.
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

Background

Despite 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.

Methods

We 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.

Results

Annual 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.

Conclusions

Decline 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

Structural 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

BACKGROUND

A 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.

METHODS

Prostate 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.

RESULTS

A 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.

CONCLUSION

It 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

BACKGROUND

Prostatic 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.

METHODS

To 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.

RESULTS

We 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.

CONCLUSIONS

The 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

Full 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

BACKGROUND: 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

Pt 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

FeCoGd(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

The 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

(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

In 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.

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(© 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

Small 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

In 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

We 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