bluuebunny/crossref_metadata_2025_split huggingface dataset:
A parameter condition for ruling out multiple equilibria of the photosynthetic carbon metabolism
Authors: Lei Hong‐Bo , Wang Xin , Wang Ruiqi , Zhu Xin‐Guang , Chen Luonan , Zhang Ji‐Feng 
Published: February 2011

AbstractIn this paper, we propose a reduced molecular network for the photosynthetic carbon metabolism, which can describe the following key characteristics: Calvin cycle, utilization of photosynthate, and photorespiration. Taking the concentrations of the nine major metabolites as variables, we represent the reduced network by deriving a nonlinear differential‐algebraic system with 48 parameters, and theoretically study the multi‐equilibrium property in the photosynthetic carbon metabolism. Specifically, we equivalently transform the original 9‐dimensional system into an independent 2‐dimensional subsystem with ten parameters, and show that the original system has no more than one physiologically feasible equilibrium when the ten parameters of the subsystem stay in a certain field around the nominal value of each parameter, no matter what values the other 38 parameters in the original model are taken. Such a theoretical result not only provides profound insights for qualitatively understanding of the dynamic features of the photosynthetic carbon metabolism, but also can be used to make an accurate judgement on a correct strategy for improving the photosynthesis in plants.Copyright © 2011 John Wiley and Sons Asia Pte Ltd and Chinese Automatic Control Society
Bounds on the optimal quantization performance of dynamically quantized linear systems with bounded noise
Authors: Ling Qiang , Gu Huihui , Lin Hai , Kang Yu 
Published: February 2011

AbstractThis paper studies a class of quantized linear control systems with diagonalizable system matrices and perturbed by bounded noise. The quantization performance of such systems is measured with the supremum of the quantization error sequence. Our goal is to improve this performance (reduce the quantization error) through designing appropriate quantization policies. Due to their efficiency, the dynamic quantization policies are considered in this paper. A lower bound on the optimal (minimum) quantization error is provided. We also propose a new quantization policy, whose quantization error is an upper bound on the optimal one. A more tractable upper quantization error bound is derived from the new policy. It is shown through simulations that the new policy's quantization error is very close to the lower bound, which confirms both the tightness of the lower bound and the efficiency of the new policy. The achieved lower and upper quantization error bounds, together with the quantization error of the new quantization policy, may provide a good indication on the optimal quantization performance.Copyright © 2011 John Wiley and Sons Asia Pte Ltd and Chinese Automatic Control Society
A deadlock prevention approach for flexible manufacturing systems with uncontrollable transitions in their Petri net models
Authors: Zhu Rongming 
Published: February 2011

AbstractDeadlocks are a highly undesired situation in a fully automated flexible manufacturing system, whose occurrences are tied to the existence of shared resources that are competed by different production processes. In the last two decades, a fair amount of research has been done on deadlock analysis and control for flexible manufacturing systems, leading to a variety of strategies in the literature. Petri nets are a promising mathematical tool to handle deadlock problems in flexible manufacturing systems. However, most deadlock control policies based on a Petri net formalism assume that all the transitions in a plant model are controllable. However, uncontrollability of events are a natural feature in a real‐world production system. This paper proposes a deadlock prevention policy for a class of Petri nets by considering the existence of uncontrollable transitions. Deadlocks are prevented by adding monitors to a plant Petri net model, whose addition does not inhibit the firings of uncontrollable transitions. Linear programming techniques are employed to find transitions to which a monitor points in order that a more permissive liveness‐enforcing Petri net supervisor can be found. A number of manufacturing examples are used to demonstrate the proposed methods.Copyright © 2011 John Wiley and Sons Asia Pte Ltd and Chinese Automatic Control Society
ExponentialH∞filtering for nonlinear discrete‐time switched stochastic systems with mixed time delays and random missing measurements
Authors: Zhang Dan , Yu Li , Zhang Wen‐An 
Published: February 2011

AbstractThis paper is concerned with the exponentialH∞filtering for a class of nonlinear discrete‐time switched stochastic hybrid systems with mixed time delays and random missing measurements. The switched system under study involves stochastic disturbance, time‐varying discrete delay, bounded distributed delay and nonlinearity. Attention is focused on the design of a mode‐dependent filter that guarantees the exponential stability in the mean‐square sense and a prescribedH∞noise attenuation level for the filtering error dynamics. By constructing a new Lyapunov functional and using the average dwell time scheme, a new delay‐dependent sufficient condition for the existence of the filter is presented in terms of linear matrix inequalities. A numerical example is finally given to show the effectiveness of the proposed design method.Copyright © 2011 John Wiley and Sons Asia Pte Ltd and Chinese Automatic Control Society
Comparison of procedures to assess non‐linear and time‐varying effects in multivariable models for survival data
Authors: Buchholz Anika , Sauerbrei Willi 
Published: February 2011

AbstractThe focus of many medical applications is to model the impact of several factors on time to an event. A standard approach for such analyses is the Cox proportional hazards model. It assumes that the factors act linearly on the log hazard function (linearity assumption) and that their effects are constant over time (proportional hazards (PH) assumption). Variable selection is often required to specify a more parsimonious model aiming to include only variables with an influence on the outcome. As follow‐up increases the effect of a variable often gets weaker, which means that it varies in time. However, spurious time‐varying effects may also be introduced by mismodelling other parts of the multivariable model, such as omission of an important covariate or an incorrect functional form of a continuous covariate. These issues interact. To check whether the effect of a variable varies in time several tests for non‐PH have been proposed. However, they are not sufficient to derive a model, as appropriate modelling of the shape of time‐varying effects is required. In three examples we will compare five recently published strategies to assess whether and how the effects of covariates from a multivariable model vary in time. For practical use we will give some recommendations.
Enhancement of recombinant human EPO production and sialylation in chinese hamster ovary cells through Bombyx mori 30Kc19 gene expression
Authors: Wang Zesong , Park Ju Hyun , Park Hee Ho , Tan Wensong , Park Tai Hyun 
Published: February 2011

AbstractProductivity and sialylation are two important factors for the production of recombinant glycoproteins in mammalian cell culture. In our previous study, we found that silkworm hemolymph increased the sialylation of recombinant secreted human placental alkaline phosphatase in the insect cells, promoted the transfer of sialic acids onto the glycoprotein oligosaccharides in an in vitro asialofetuin sialylation system, and enhanced recombinant protein production in the Chinese hamster ovary (CHO) cells. These beneficial effects were mainly due to the 30K proteins, which consist of five isoforms. Among the 30K proteins, 30Kc19 was determined to be the major component. In this study, the 30Kc19 gene was introduced into a CHO cell line producing recombinant human erythropoietin, and its effects on productivity and sialylation were investigated. The transient expression of 30Kc19 significantly improved the production and sialylation of EPO. A stable cell line containing 30Kc19 was also established to investigate the effect of 30Kc19 gene expression. The stable expression of 30Kc19 increased the production and sialylation by 102.6% and 87.1%, respectively. The enhanced productivity from 30Kc19 expression is believed to occur because the 30Kc19 protein suppresses the loss of mitochondrial membrane potential and consequently improves the generation of intracellular ATP. In addition, the positive effect of 30Kc19 expression on sialylation is believed to be due to its ability to maintain sialyltransferase activity. In conclusion, 30Kc19 expression is a novel approach to improve the production and sialylation of recombinant glycoproteins in CHO cells. Biotechnol. Bioeng. 2011; 108:1634–1642. © 2011 Wiley Periodicals, Inc.
Glycoside hydrolase inventory drives plant polysaccharide deconstruction by the extremely thermophilic bacterium Caldicellulosiruptor saccharolyticus
Authors: VanFossen Amy L. , Ozdemir Inci , Zelin Samantha L. , Kelly Robert M. 
Published: February 2011

AbstractThe genome of Caldicellulosiruptor saccharolyticus encodes a range of glycoside hydrolases (GHs) that mediate plant biomass deconstruction by this bacterium. Two GH‐based genomic loci that appear to be central to the hydrolysis of hemicellulosic and cellulosic substrates were examined. XynB‐XynF (Csac_2404‐Csac_2411) encodes intracellular and extracellular GHs that are active towards xylan and xylan side‐chains, as well as carboxymethyl cellulose (CMC). XynD (Csac_2409) and XynE (Csac_2410) were produced recombinantly and confirmed to be xylanases. XynF (Csac_2411) was produced in two separate polypeptides, each with one GH43 catalytic domain displaying α‐L‐arabinofuranosidase activity. CelA‐ManB (Csac_1076‐Csac_1080) encodes four multi‐domain, extracellular GHs, including CelB (Csac_1078), a 118 kDa extracellular enzyme not present in the other genome‐sequenced member of this genus, Caldicellulosiruptor bescii (formerly Anaerocellum thermophilum). CelB contains both GH10 and GH5 domains, separated by a family 3 carbohydrate‐binding module (CBM3). CelB encoded in Csac_1078 differed from the version originally reported (Saul et al., 1990, Appl Environ Microbiol 56:3117–3124) with respect to linker regions. CelB hydrolyzed xylan and CMC, as well as barley β‐glucan, glucomannan, and arabinoxylan. For all substrates tested, intact CelB was significantly more active than either the individual GH5 and GH10 domains or the two discrete domains together, indicating that the multi‐domain architecture is essential for complex carbohydrate hydrolysis. Transcriptomes for C. saccharolyticus grown at 70°C on glucose, xylose, xyloglucan, switchgrass, and poplar revealed that certain GHs were particularly responsive to growth on switchgrass and poplar and that CelB was in the top decile of all transcripts during growth on the plant biomass. Biotechnol. Bioeng. 2011; 108:1559–1569. © 2011 Wiley Periodicals, Inc.
Model‐based analysis of the role of biological, hydrological and geochemical factors affecting uranium bioremediation
Authors: Zhao Jiao , Scheibe Timothy D. , Mahadevan R. 
Published: February 2011

AbstractUranium contamination is a serious concern at several sites motivating the development of novel treatment strategies such as the Geobacter‐mediated reductive immobilization of uranium. However, this bioremediation strategy has not yet been optimized for the sustained uranium removal. While several reactive‐transport models have been developed to represent Geobacter‐mediated bioremediation of uranium, these models often lack the detailed quantitative description of the microbial process (e.g., biomass buildup in both groundwater and sediments, electron transport system, etc.) and the interaction between biogeochemical and hydrological process. In this study, a novel multi‐scale model was developed by integrating our recent model on electron capacitance of Geobacter (Zhao et al., 2010) with a comprehensive simulator of coupled fluid flow, hydrologic transport, heat transfer, and biogeochemical reactions. This mechanistic reactive‐transport model accurately reproduces the experimental data for the bioremediation of uranium with acetate amendment. We subsequently performed global sensitivity analysis with the reactive‐transport model in order to identify the main sources of prediction uncertainty caused by synergistic effects of biological, geochemical, and hydrological processes. The proposed approach successfully captured significant contributing factors across time and space, thereby improving the structure and parameterization of the comprehensive reactive‐transport model. The global sensitivity analysis also provides a potentially useful tool to evaluate uranium bioremediation strategy. The simulations suggest that under difficult environments (e.g., highly contaminated with U(VI) at a high migration rate of solutes), the efficiency of uranium removal can be improved by adding Geobacter species to the contaminated site (bioaugmentation) in conjunction with the addition of electron donor (biostimulation). The simulations also highlight the interactive effect of initial cell concentration and flow rate on U(VI) reduction. Biotechnol. Bioeng. 2011; 108:1537–1548. © 2011 Wiley Periodicals, Inc.
Effects of bacteriophage on the surface properties of chalcopyrite (CuFeS2), and phage‐induced flocculation of chalcopyrite, glacial till, and oil sands tailings
Authors: Curtis Susan B. , MacGillivray Ross T.A. , Dunbar W. Scott 
Published: February 2011

AbstractThe binding of mineral‐specific phage to the surface of chalcopyrite (CuFeS2) was investigated by using X‐ray photoelectron spectroscopy and scanning Auger microscopy. These studies confirmed the elemental composition of the minerals and confirmed that bacteriophage were bound to the mineral surface. These techniques also revealed that the phage were not forming a continuous film over the entire surface of the CuFeS2 particles, but selectively bound to the slimes coating the particles. In addition, the effect of mineral‐specific phage binding to the surface of CuFeS2 was investigated using induction time and zeta potential measurements. Bacteriophage (1012/mL) increased the induction time (contact time resulting in 50% particle attachment to a bubble) from ∼7.5 to ∼17 ms and reversed the zeta potential from negative to positive. In the course of performing the zeta potential measurements on particles <45 µm in diameter, phage‐induced aggregation was observed. The mechanism of aggregation was explored using a range of pH (3–11) and cation concentrations. Aggregation was observed across the tested pH range and with all cations. Phage also mediated aggregation of glacial till and oil sands tailings in a dose‐dependent and particle size‐dependent manner. We conclude that binding of bacteriophage to the surface of CuFeS2 does alter its surface properties. Biotechnol. Bioeng. 2011; 108:1579–1590. © 2011 Wiley Periodicals, Inc.
Carbohydrate nanoparticle‐mediated colloidal assembly for prolonged efficacy of bacteriocin against food pathogen
Authors: Bi Lin , Yang Lei , Bhunia Arun K. , Yao Yuan 
Published: February 2011

AbstractThe goal of this study was to demonstrate the ability of carbohydrate nanoparticle‐stabilized emulsion to prolong the efficacy of bacteriocin against food pathogens. An amphiphilic, negatively charged carbohydrate nanoparticle, phytoglycogen octenyl succinate (PG‐OS), was used to form oil‐in‐water emulsion for delivering bacteriocin nisin against the food pathogen Listeria monocytogenes. Dynamic light scattering test showed that in emulsion all PG‐OS nanoparticles were adsorbed at the surface of oil droplets. Zeta‐potential analysis indicated an effective adsorption of positively charged nisin molecules at the surface of PG‐OS interfacial layer. Nisin depletion model showed that, during 50 days of storage, the anti‐listerial activity of nisin‐containing PG‐OS‐stabilized emulsion was substantially greater than that of nisin solution. In contrast, the emulsion stabilized with a neutral, small‐molecule surfactant (Tween 20) or negatively charged, hyperbranched carbohydrate polymer (modified starch) was either ineffective or less effective than the nanoparticle‐stabilized emulsion to retain nisin activity during storage. Biotechnol. Bioeng. 2011; 108:1529–1536. © 2011 Wiley Periodicals, Inc.
Improvement of HepG2/C3a cell functions in a microfluidic biochip
Authors: Prot Jean Matthieu , Aninat Caroline , Griscom Laurent , Razan Florence , Brochot Céline , Guillouzo Christiane Guguen , Legallais Cécile , Corlu Anne , Leclerc Eric 
Published: February 2011

AbstractCurrent developments in tissue engineering and microtechnology fields allow the use of microfluidic biochip as microtools for in vitro investigations. In the present study, we describe the behavior of HepG2/C3a cells cultivated in a poly(dimethylsiloxane) (PDMS) microfluidic biochip coupled to a perfusion system. Cell culture in the microfluidic biochip for 96 h including 72 h of perfusion provoked a 24 h delay in cell growth compared to plate cultures. Inside the microfluidic biochip, few apoptosis, and necrosis were detected along the culture and 3D cell organization was observed. Regarding the hepatic metabolism, glucose and glutamine consumptions as well as albumin synthesis were maintained. A transcriptomic analysis performed at 96 h of culture using Affymetrix GeneChip demonstrated that 1,025 genes with a fold change above 1.8 were statistically differentially expressed in the microfluidic biochip cultures compared to plate cultures. Among those genes, phase I enzymes involved in the xenobiotic's metabolism such as the cytochromes P450 (CYP) 1A1/2, 2B6, 3A4, 3A5, and 3A7 were up‐regulated. The CYP1A1/2 up‐regulation was associated with the appearance of CYP1A1/2's activity evidenced by using EROD biotransformation assay. Several phase II enzymes such as sulfotransferases (SULT1A1 and SULT1A2), UDP‐glucuronyltransferase (UGT1A1, UGT2B7) and phase III transporters (such as MDR1, MRP2) were also up‐regulated. In conclusion, microfluidic biochip could and provide an important insight to exploring the xenobiotic's metabolism. Altogether, these results suggest that this kind of biochip could be considered as a new pertinent tool for predicting cell toxicity and clearance of xenobiotics in vitro. Biotechnol. Bioeng. 2011; 108:1704–1715. © 2011 Wiley Periodicals, Inc.
Combining Aminocyanine Dyes with Polyamide Dendrons: A Promising Strategy for Imaging in the Near‐Infrared Region
Authors: Ornelas Cátia , Lodescar Rachelle , Durandin Alexander , Canary James W. , Pennell Ryan , Liebes Leonard F. , Weck Marcus 
Published: February 2011

AbstractCyanine dyes are known for their fluorescence in the near‐IR (NIR) region, which is desirable for biological applications. We report the synthesis of a series of aminocyanine dyes containing terminal functional groups such as acid, azide, and cyclooctyne groups for further functionalization through, for example, click chemistry. These aminocyanine dyes can be attached to polyfunctional dendrons by copper‐catalyzed azide alkyne cycloaddition (CuAAC), strain‐promoted azide alkyne cycloaddition (SPAAC), peptide coupling, or direct SNR1 reactions. The resulting dendron–dye conjugates were obtained in high yields and displayed high chemical stability and photostability. The optical properties of the new compounds were studied by UV/Vis and fluorescence spectroscopy. All compounds show large Stokes shifts and strong fluorescence in the NIR region with high quantum yields, which are optimal properties for in vivo optical imaging.
Amine Exchange in Formamidines: An Experimental and Theoretical Study
Authors: Capela Marinha dF. , Mosey Nicholas J. , Xing Liyan , Wang Ruiyao , Petitjean Anne 
Published: February 2011

AbstractNH‐containing formamidines combine a reasonably strong association to carboxylic acids to form complexes of well‐defined geometries with a simultaneous proton‐induced electrophilicity enhancement that allows for the exchange of their amine portion. The NC(H)NH fragment, therefore, undergoes “imine‐like” exchange with N‐containing nucleophiles. Because of the prototropic equilibrium, the NC(H)NH fragment may behave as a “bisimine” centred on the same carbon, in which both N‐containing fragments can be exchanged. Considering the proton‐induced sensitisation of both CN units and the well‐defined formamidine–carboxylic acid complex geometry, it should be possible to use carboxylic acids as templates for the synthesis of defined architectures by dynamic amine exchange within formamidines. This study highlights three exchange regimes based on the nature of the incoming amine (aliphatic amines, aromatic amines and alkoxyamines), as well as exchange rules based on the amine leaving groups. Following this analysis, a proof of concept for carboxylic acid templated macrocycle formation through dynamic exchange is provided.
Highly Crystalline and Conductive Nitrogen‐Doped Mesoporous Carbon with Graphitic Walls and Its Electrochemical Performance
Authors: Datta Kasibhatta K. R. , Balasubramanian Veerappan V. , Ariga Katsuhiko , Mori Toshiyuki , Vinu Ajayan 
Published: February 2011

AbstractWe present a rational and simple methodology to fabricate highly conductive nitrogen‐doped ordered mesoporous carbon with a graphitic wall structure by the simple adjustment of the carbonization temperature of mesoporous carbon nitride without the addition of any external nitrogen sources. By simply controlling the heat‐treatment temperature, the structural order and intrinsic properties such as surface area, conductivity, and pore volume, and the nitrogen content of ordered graphitic mesoporous carbon can be controlled. Among the materials studied, the sample heat‐treated at 1000 °C shows the highest conductivity, which is 32 times higher than that for the samples treated at 800 °C and retains the well‐ordered mesoporous structure of the parent mesoporous carbon nitride and a reasonable amount of nitrogen in the graphitic framework. Since these materials exhibit high conductivity with the nitrogen atoms in the graphitic framework, we further demonstrate their use as a support for nanoparticle fabrication without the addition of any external stabilizing or size‐controlling agent, as well as the anode electrode catalysts. Highly dispersed platinum nanoparticles with a size similar to that of the pore diameter of the support can be fabricated since the nitrogen atoms and the well‐ordered porous structure in the mesoporous graphitic carbon framework act as a stabilizing and size‐controlling agent, respectively. Furthermore the Pt‐loaded, nitrogen‐doped mesoporous graphitic carbon sample with a high conductivity shows much higher anodic electrocatalytic activity than the other materials used in the study.
Unusual Inversion Phenomenon of β‐Cyclodextrin Dimers in Water
Authors: Menuel Stéphane , Azaroual Nathalie , Landy David , Six Natacha , Hapiot Frédéric , Monflier Eric 
Published: February 2011

AbstractA conformational analysis of three triazole‐containing bridged bis‐β‐ cyclodextrins (CD) has been carried out to evaluate their recognition ability. NMR spectroscopy and ITC measurements clearly demonstrate that one of the CD glucopyranose units undergoes a 360° rotation in water so that the spacer linking the two CDs is deeply included into one of the CD cavities. The amplitude of this inversion phenomenon depends on the nature of the spacer and results in a limited accessibility to the CD cavities in line with previous catalytic results.