bluuebunny/crossref_metadata_2025_split huggingface dataset:
Reversible Photoinduced Switching of Permeability in a Cast Non‐Porous Film Comprising Azobenzene Liquid Crystalline Polymer
Authors: Liu Jian , Wang Mingle , Dong Mingling , Gao Liude , Tian Jingjing 
Published: July 2011

AbstractPermeation characteristics of an azobenzene‐containing liquid crystalline (LC) non‐porous film are investigated using a metallic corrosion method. Thin films (300 nm) are fabricated by the solution casting of an azobenzene side‐chain LC polymer on freshly polished carbon steel coupons. Coated coupons are treated under the following conditions: a) gradual annealing at a cooling rate lower than 1 °C · min−1 from 150 °C (above its Tg) to room temperature, and b) irradiation at 465 nm (20 mW · cm−2) with either circularly polarized light (CPL) or non‐polarized light (NPL). The morphology of these films is characterized using X‐ray diffraction, polarized optical microscopy, and transmission measurements. The results suggest that the annealing treatment resulted in the formation of a polydomain structure consisting of locally ordered small smectic domains that lack mutual orientation. Ordered micro domains are surrounded by disordered phases. CPL and NPL irradiation generates a monodomain orientated structure and an isotropic liquid crystal glass, respectively. The permeability of these non‐porous films treated by CPL, NPL, and annealing are found to be 6.14 × 10−4, 1.92 × 10−2, and 1.56 × 10−3 cm3 · m−2 · d−1. An orientation‐dependent structure model is constructed to explain the permeation phenomenon, considering the ordered phase is impermeable, only the disordered phase is accessible to penetrating molecules. Fast switching of gas permeation is demonstrated by alternative irradiation of the film with CPL and NPL, which results in an approximately 30‐fold difference in the permeability of the non‐porous film.magnified image
Simulations of Blood Flow in Plain Cylindrical and Constricted Vessels with Single Cell Resolution
Authors: Janoschek Florian , Toschi Federico , Harting Jens 
Published: July 2011

AbstractUnderstanding the physics of blood is challenging due to its nature as a suspension of soft particles and the fact that typical problems involve different scales. This is valid also for numerical investigations. In fact, many computational studies either neglect the existence of discrete cells or resolve relatively few cells very accurately. The authors recently developed a simple and highly efficient yet still particulate model with the aim to bridge the gap between currently applied methods. The present work focuses on its applicability to confined flows in vessels of diameters up to ≈100 µm. For hematocrit values below 30%, a dependence of the apparent viscosity on the vessel diameter in agreement with experimental literature data is found.magnified image
Characteristic Times of Polymer Tumbling Under Shear Flow
Authors: Usabiaga Florencio Balboa , Delgado‐Buscalioni Rafael 
Published: July 2011

AbstractThe tumbling dynamics of flexible chains in shear flow, analysed by Brownian Dynamics simulations, are found to be ruled by three characteristic times τtumb, τdif and τlag. The average tumbling time τtumb scales with the shear rate with a robust exponent against excluded volume (EV) or hydrodynamic interactions, $\tau _{{\rm tumb}} \approx {\dot {\gamma }}^{{-} 2/3} $. The chain extensions in the flow plane decorrelate in a time τdif determined by the diffusion of the chain configuration in gradient direction, $\tau _{{\rm dif}} \approx Y^{2} /D$. The chain keeps memory of its configuration over a number of tumblings events given by the ratio τdif/τtumb. While for ideal chains $\tau _{{\rm dif}} /\tau _{{\rm tumb}} \approx O(1)$, for expanded (EV) chains we find $\tau _{{\rm dif}} /\tau _{{\rm tumb}} \approx {\dot {\gamma }}^{0.2} $. Hence, EV chains tumble in a more deterministic way as ${\dot {\gamma }}$ is increased. As a consequence, contrary to previous assumptions, the exponential tail of the tumbling time distribution $P(\tau )\approx {\exp} ({-} \nu \tau )$ presents a non‐Poissonian exponent. This exponent ν is found to be determined by a new characteristic time τlag measuring how fast the chain in‐flow elongation X responses to the drag force induced by chain fluctuations in gradient direction Y. PSCS numbers.magnified image
A Simulation Model of Biofilms with Autonomous Cells, 2 ‐ Explicit Representation of the Extracellular Polymeric Substance
Authors: Tao Yu‐Guo , Slater Gary W. 
Published: July 2011

AbstractBiofilms are complex colonies of bacteria that grow in contact with a wall, often in the presence of a water flow. In the current work, biofilm colony growth is investigated using a two‐dimensional lattice Monte–Carlo algorithm based on the bond‐fluctuation algorithm (BFA). One of the distinguishing characteristics of biofilms, the synthesis and physical properties of the extracellular polymeric substance (EPS) in which the cells are embedded, is explicitly taken into account. Cells are modeled as autonomous closed loops with well‐defined mechanical and biological properties, while the EPS is modeled as flexible polymeric chain synthesized by the cells during their growth. By tuning the structural, energy, biological, and morphologic parameters of the model, the cell shapes as well as the growth and maturation of various types of biofilm colonies (including colonies with multiple species) can be controlled.magnified image
Polymerization Reactor Modeling in Industry
Authors: Mueller Philipp A. , Richards John R. , Congalidis John P. 
Published: July 2011

AbstractThis paper provides an industrial perspective for the development of polymer reaction engineering models and their application to create new materials, products, and improved or novel processes. The challenges specific to polymer reactor modeling are discussed in the context of articles and books that the authors have found useful. Four components of a polymer reactor model (kinetics, thermodynamics, transport effects, and particle dynamics) are discussed with illustrative examples. Finally typical outputs of polymer reactor models are shown to demonstrate that a first principles model supported and validated by experiments can be a very powerful tool for fundamental understanding of polymer reactors and is a recommended alternative to empirical methods and experimentation alone.magnified image
Comparative effectiveness of individual angiotensin receptor blockers on risk of mortality in patients with chronic heart failure
Authors: Desai Rishi J. , Ashton Carol M. , Deswal Anita , Morgan Robert O. , Mehta Hemalkumar B. , Chen Hua , Aparasu Rajender R. , Johnson Michael L. 
Published: July 2011

ABSTRACTObjectiveThere is little evidence on comparative effectiveness of individual angiotensin receptor blockers (ARBs) in patients with chronic heart failure (CHF). This study compared four ARBs in reducing risk of mortality in clinical practice.MethodsA retrospective analysis was conducted on a national sample of patients diagnosed with CHF from 1 October 1996 to 30 September 2002 identified from Veterans Affairs electronic medical records, with supplemental clinical data obtained from chart review. After excluding patients with exposure to ARBs within the previous 6 months, four treatment groups were defined based on initial use of candesartan, valsartan, losartan, and irbesartan between the index date (1 October 2000) and the study end date (30 September 2002). Time to death was measured concurrently during that period. A marginal structural model controlled for sociodemographic factors, comorbidities, comedications, disease severity (left ventricular ejection fraction), and potential time‐varying confounding affected by previous treatment (hospitalization). Propensity scores derived from a multinomial logistic regression were used as inverse probability of treatment weights in a generalized estimating equation to estimate causal effects.ResultsAmong the 1536 patients identified on ARB therapy, irbesartan was most frequently used (55.21%), followed by losartan (21.74%), candesartan (15.23%), and valsartan (7.81%). When compared with losartan, after adjusting for time‐varying hospitalization in marginal structural model, candesartan (OR = 0.79, 95%CI = 0.42–1.50), irbesartan (OR = 1.17, 95%CI = 0.72–1.90), and valsartan (OR = 0.98, 95%CI = 0.45–2.14) were found to have similar effectiveness in reducing mortality in CHF patients.ConclusionEffectiveness of ARBs in reducing mortality is similar in patients with CHF in everyday clinical practice. Copyright © 2011 John Wiley & Sons, Ltd.
Development of gallium gradients in three‐stage Cu(In,Ga)Se2 co‐evaporation processes
Authors: Schleussner Sebastian Michael , Törndahl Tobias , Linnarsson Margareta , Zimmermann Uwe , Wätjen Timo , Edoff Marika 
Published: July 2011

ABSTRACTWe use secondary‐ion mass spectrometry, X‐ray diffraction and scanning electron microscopy to investigate the development over time of compositional gradients in Cu(In,Ga)Se2 thin films grown in three‐stage co‐evaporation processes and suggest a comprehensive model for the formation of the well‐known ‘notch’ structure. The model takes into account the need for compensating Cu diffusion by movement of group‐III ions in order to remain on the quasi‐binary tie line and indicates that the mobilities of In and Ga ions differ. Cu diffuses towards the back in the second stage and towards the front in the third, and this is the driving force for the movement of In and Ga. The [Ga]/[In + Ga] ratio then increases in the direction of the respective Cu movement because In has a higher mobility at process conditions than has Ga. Interdiffusion of In and Ga can be considerable in the (In,Ga)2Se3 film of the first stage, but seems largely to cease in Cu(In,Ga)Se2 and shows no signs of being boosted by the presence of a Cu2Se layer. Copyright © 2011 John Wiley & Sons, Ltd.
Use of support vector regression and numerically predicted cloudiness to forecast power output of a photovoltaic power plant in Kitakyushu, Japan
Authors: da Silva Fonseca Joao Gari , Oozeki Takashi , Takashima Takumi , Koshimizu Gentarou , Uchida Yoshihisa , Ogimoto Kazuhiko 
Published: July 2011

ABSTRACTThe development of a methodology to forecast accurately the power produced by photovoltaic systems can be an important tool for the dissemination and integration of such systems on the public electricity grids. Thus, the objective of this study was to forecast the power production of a 1‐MW photovoltaic power plant in Kitakyushu, Japan, using a new methodology based on support vector machines and on the use of several numerically predicted weather variables, including cloudiness. Hourly forecasts of the power produced for 1 year were carried out. Moreover, the effect of the use of numerically predicted cloudiness on the quality of the forecasts was also investigated. The forecasts of power production obtained with the proposed methodology had a root mean square error of 0.0948 MW h and a mean absolute error of 0.058 MW h. It was also found that the forecast and measured values of power production had a good level of correlation varying from 0.8 to 0.88 according to the season of the year. Finally, the use of numerically predicted cloudiness had an important role in the accuracy of the forecasts, and when cloudiness was not used, the root mean square error of the forecasts increased more than 32%, and the mean absolute error increased more than 42%. Copyright © 2011 John Wiley & Sons, Ltd.
Evaluation of two‐dimensional electrical properties of photovoltaic modules using bias‐dependent electroluminescence
Authors: Li Biao , Stokes Adam , Doble Dan M. J. 
Published: July 2011

ABSTRACTAn approach to deriving two‐dimensional maps of cell and module electrical properties from electroluminescence imaging is presented. The technique involves quantitative comparison of the intensity differences in the electroluminescence images at different bias currents, enabling the derivation of junction voltages of individual pixels. These data were then fitted to a distributed electrical model that allows the derivation of a two‐dimensional dark I–V curve for each point across the module. Interpretation of the dark I–V curve enabled the evaluation of series resistance, shunt resistance, ideality factor, and reverse saturation current for each pixel. These parameters were then used to enable the prediction of module performance under illumination. Copyright © 2011 John Wiley & Sons, Ltd.
Exploration of Atmospheric Pressure Plasma Nanofilm Technology for Straightforward Bio‐Active Coating Deposition: Enzymes, Plasmas and Polymers, an Elegant Synergy
Authors: Heyse Pieter , Van Hoeck Arne , Roeffaers Maarten B. J. , Raffin Jean‐Paul , Steinbüchel Alexander , Stöveken Tim , Lammertyn Jeroen , Verboven Pieter , Jacobs Pierre A. , Hofkens Johan , Paulussen Sabine , Sels Bert F. 
Published: July 2011

AbstractWhile protein or enzyme immobilization methodologies are readily applicable in a majority of industrial processes, some lacunas still remain. For example, the multi‐step, wet‐chemical nature of current immobilization reactions limits straightforward bio‐film fabrication in continuous production units. As such, a fast and preferably single step immobilization technique, minimizing solvent use and decoupling deposition substrate from used method is awaited. In this research, an atmospheric pressure plasma reaction environment is chosen for its flexibility in terms of reactivity and the ease of coating depositions on a wide variety of substrates. Organic coating precursors such as acetylene or pyrrole are injected simultaneously with an atomized enzyme solution directly in the discharge. By atomizing the enzyme solution, the enzyme molecules are surrounded by a watery shell. It is envisioned that such droplet act as “shuttles”, delivering the enzymes to the discharge while protecting them from the harsh plasma conditions. In the discharge, polymerization of the added organic coating precursor takes place and consequently, the enzyme molecules become trapped in the growing polymer network. In addition, atomization of the protein solution favors the spatial distribution of the proteins in the coating. Several enzymes are evaluated and enhanced temperature and solvent stability is observed. Moreover, single molecule fluorescence, enzyme activity and bio‐recognition experiments demonstrate protein integrity after plasma assisted immobilization.magnified image
Optimization of an Analytical Procedure for Extraction of Lipids from Microalgae
Authors: Ryckebosch Eline , Muylaert Koenraad , Foubert Imogen 
Published: July 2011

AbstractAn optimized procedure for extraction of total and non‐polar lipids from microalgae is proposed. The effects of solvent, pretreatment (lyophilization, inactivation of lipases, and addition of antioxidants) and cell‐disruption (liquid nitrogen, sonication, and bead beating) on total lipid content, lipid class, and fatty acid composition were examined. Chloroform–methanol 1:1 was shown to be the best solvent mixture for extraction of total lipids from microalgae. When performing this extraction, lyophilized algae can be used, no pretreatment with isopropanol to inactivate the lipases is needed and addition of antioxidants is not necessary. Furthermore, cell‐disruption is not essential, although in that case two extractions must be performed in series to ensure that, irrespective of the microalgal species, all lipids are extracted. Determination of non‐polar lipid content should be performed by separation of the total lipid extract on an SPE column. Extraction using petroleum ether is only appropriate when a bead beater is used for pretreatment.
Ghrelin levels are reduced in Rett syndrome patients with eating difficulties
Authors: Hara Munetsugu , Nishi Yoshihiro , Yamashita Yushiro , Yoh Junko , Takahashi Satoru , Nagamitsu Shin‐ichiro , Kakuma Tatsuyuki , Hosoda Hiroshi , Kangawa Kenji , Kojima Masayasu , Matsuishi Toyojiro 
Published: July 2011

AbstractMost patients with Rett syndrome (RTT) have both gastrointestinal problems and somatic growth failure, including microcephaly. Ghrelin is a peptide hormone involved in growth hormone secretion, interdigestive motility, and feeding behavior. Plasma ghrelin assays have previously been described for other neurodevelopmental disorders. To examine the pathophysiology of RTT, we measured plasma levels of ghrelin in patients with RTT. A case–control study examining plasma levels of ghrelin, serum growth hormone, and insulin‐like growth factor‐1 (IGF‐1) was performed on 27 patients with RTT and 53 controls. Plasma levels of total (T)‐ and octanoyl (O)‐ghrelin were significantly lower in patients with RTT than in controls. Plasma levels of T‐ghrelin correlated significantly with serum IGF‐1 levels and head circumference. Significantly lower levels of plasma T‐ghrelin and O‐ghrelin were observed in RTT patients with eating difficulties, while lower levels of plasma T‐ghrelin were observed in RTT patients with constipation, in comparison to patients without either of these symptoms. Alterations in plasma ghrelin levels may reflect various clinical symptoms and signs in RTT patients, including growth failure, acquired microcephalus, autonomic nerve dysfunction, and feeding difficulties. We describe the role of ghrelin in RTT and suggest this peptide as a novel biological marker in patients with RTT.
Identifying disease-associated SNP clusters via contiguous outlier detection
Authors: Yang Can , Zhou Xiaowei , Wan Xiang , Yang Qiang , Xue Hong , Yu Weichuan 
Published: July 2011

Abstract
Motivation: Although genome-wide association studies (GWAS) have identified many disease-susceptibility single-nucleotide polymorphisms (SNPs), these findings can only explain a small portion of genetic contributions to complex diseases, which is known as the missing heritability. A possible explanation is that genetic variants with small effects have not been detected. The chance is &lt; 8 that a causal SNP will be directly genotyped. The effects of its neighboring SNPs may be too weak to be detected due to the effect decay caused by imperfect linkage disequilibrium. Moreover, it is still challenging to detect a causal SNP with a small effect even if it has been directly genotyped.
Results: In order to increase the statistical power when detecting disease-associated SNPs with relatively small effects, we propose a method using neighborhood information. Since the disease-associated SNPs account for only a small fraction of the entire SNP set, we formulate this problem as Contiguous Outlier DEtection (CODE), which is a discrete optimization problem. In our formulation, we cast the disease-associated SNPs as outliers and further impose a spatial continuity constraint for outlier detection. We show that this optimization can be solved exactly using graph cuts. We also employ the stability selection strategy to control the false positive results caused by imperfect parameter tuning. We demonstrate its advantage in simulations and real experiments. In particular, the newly identified SNP clusters are replicable in two independent datasets.
Availability: The software is available at: http://bioinformatics.ust.hk/CODE.zip.
Contact: eeyu@ust.hk
Supplementary information: Supplementary data are available at Bioinformatics online.
GenSSI: a software toolbox for structural identifiability analysis of biological models
Authors: Chiş Oana , Banga Julio R. , Balsa-Canto Eva 
Published: July 2011

Abstract
Summary: Mathematical modeling has a key role in systems biology. Model building is often regarded as an iterative loop involving several tasks, among which the estimation of unknown parameters of the model from a certain set of experimental data is of central importance. This problem of parameter estimation has many possible pitfalls, and modelers should be very careful to avoid them. Many of such difficulties arise from a fundamental (yet often overlooked) property: the so-called structural (or a priori) identifiability, which considers the uniqueness of the estimated parameters. Obviously, the structural identifiability of any tentative model should be checked at the beginning of the model building loop. However, checking this property for arbitrary non-linear dynamic models is not an easy task. Here we present a software toolbox, GenSSI (Generating Series for testing Structural Identifiability), which enables non-expert users to carry out such analysis. The toolbox runs under the popular MATLAB environment and is accompanied by detailed documentation and relevant examples.
Availability: The GenSSI toolbox and the related documentation are available at http://www.iim.csic.es/%7Egenssi.
Contact: ebalsa@iim.csic.es
Structural analysis of the hot spots in the binding between H1N1 HA and the 2D1 antibody: do mutations of H1N1 from 1918 to 2009 affect much on this binding?
Authors: Liu Qian , Hoi Steven C. H. , Su Chinh T. T. , Li Zhenhua , Kwoh Chee-Keong , Wong Limsoon , Li Jinyan 
Published: July 2011

Abstract
Motivation: Worldwide and substantial mortality caused by the 2009 H1N1 influenza A has stimulated a new surge of research on H1N1 viruses. An epitope conservation has been learned in the HA1 protein that allows antibodies to cross-neutralize both 1918 and 2009 H1N1. However, few works have thoroughly studied the binding hot spots in those two antigen–antibody interfaces which are responsible for the antibody cross-neutralization.
Results: We apply predictive methods to identify binding hot spots at the epitope sites of the HA1 proteins and at the paratope sites of the 2D1 antibody. We find that the six mutations at the HA1's epitope from 1918 to 2009 should not harm its binding to 2D1. Instead, the change of binding free energy on the whole exhibits an increased tendency after these mutations, making the binding stronger. This is consistent with the observation that the 1918 H1N1 neutralizing antibody can cross-react with 2009 H1N1. We identified three distinguished hot spot residues, including Lys166, common between the two epitopes. These common hot spots again can explain why 2D1 cross-reacted. We believe that these hot spot residues are mutation candidates which may help H1N1 viruses to evade the immune system. We also identified eight residues at the paratope site of 2D1, five from its heavy chain and three from its light chain, that are predicted to be energetically important in the HA1 recognition. The identification of these hot spot residues and their structural analysis are potentially useful to fight against H1N1 viruses.
Contact: jinyan.li@uts.edu.au
Availability: Z-score is available at http://155.69.2.25/liuqian/indexz.py
Supplementary information: Supplementary data are available at Bioinformatics online.
phyloMeta: a program for phylogenetic comparative analyses with meta-analysis
Authors: Lajeunesse Marc J. 
Published: July 2011

AbstractSummary: phyloMeta is an easy to use console program for integrating phylogenetic information into meta-analysis. It is designed to help ecologists, evolutionary biologists and conservation biologists analyze effect size data extracted from published studies in a comparative phylogenetic context. This software estimates phylogenetic versions of all the traditional meta-analytical statistics used for: pooling effect sizes with weighted regressions; evaluating the homogeneity of these effect sizes; performing moderator tests akin to ANOVA style analyses; and analyzing data with fixed- and random-effects models. phyloMeta is developed in C/C++ and can be used via command line in MS Windows environments.Availability: phyloMeta can be obtained freely as an executable on the web at http://lajeunesse.myweb.usf.edu/publicationsContact: lajeunesse@usf.edu