bluuebunny/crossref_metadata_2025_split huggingface dataset:
Describing Ordinal Odds Ratios for Stratifiedr×cTables
Authors: Liu Ivy 
Published: September 2003

AbstractFor anr×ctable with ordinal responses, odds ratios are commonly used to describe the relationship between the row and column variables. This article shows two types of ordinal odds ratios where local‐global odds ratios are used to compare several groups on ac‐category ordinal response and a global odds ratio is used to measure the global association between a pair of ordinal responses. When there is a stratification factor, we consider Mantel‐Haenszel (MH) type estimators of these odds ratios to summarize the association from several strata. Like the ordinary MH estimator of the common odds ratio for several 2 × 2 contingency tables, the estimators are used when the association is not expected to vary drastically among the strata. Also, the estimators are consistent under the ordinary asymptotic framework in which the number of strata is fixed and also under sparse asymptotics in which the number of strata grows with the sample size. Compared to the maximum likelihood estimators, simulations find that the MH type estimators perform better especially when each stratum has few observations. This article provides variances and covariances formulae for the local‐global odds ratios estimators and applies the bootstrap method to obtain a standard error for the global odds ratio estimator. At the end, we discuss possible ways of testing the homogeneity assumption.
A note on the Design of Unreplicated Trials
Authors: Williams E.R. , John J.A. 
Published: September 2003

AbstractOne approach to the design of early generation trials is to have a number of replicated check varieties and a larger number of unreplicated or new varieties. For such trials we define the class of α–α‐designs as an extension to the augmented lattice square designs of Federer (2002). Efficient latinized α–α‐designs can be conveniently constructed using the design generation package CycDesigN.
A Stochastic Model Relating the Number of Cells at X‐Inactivation to the Allelic Ratio in Normal Heterozygous Adult Females
Authors: Chen George S. , Chen Shande 
Published: September 2003

AbstractEarly in development, one X‐chromosome in each cell of the female embryo is inactivated. Knowing the number of certain human tissue cells at the time of X‐inactivation can improve our understanding of certain diseases such as cancer or genetic disorders as well as cellular development. However, the moment of X‐inactivation in humans is difficult to observe directly. In this study, we developed a mathematical model using branching processes and asymptotic normal approximation that will more accurately determine a relationship between the number of cells at X‐inactivation with the proportion of one allele found in normal heterozygous adult females. We then conducted computer simulations to show the adequacy of this model. Finally, this model was used to more accurately estimate the number of hemopoietic stem cells at X‐inactivation using a real life data set.
Multiple Comparisons in Nonlinear Repeated Measurements
Authors: Hyakutake Hiroto 
Published: September 2003

AbstractIt is interest to compare functions of parameters in nonlinear models for repeated measurements. In a pharmacokinetic model, the maximum value of the model would be a nonlinear function of some unknown parameters. In this paper, simultaneous confidence intervals of functions of parameters in a nonlinear model for repeated mesurement data are considered to compare the populations.
Analysis of Escherichia coli anaplerotic metabolism and its regulation mechanisms from the metabolic responses to altered dilution rates and phosphoenolpyruvate carboxykinase knockout
Authors: Yang Chen , Hua Qiang , Baba Tomoya , Mori Hirotada , Shimizu Kazuyuki 
Published: September 2003

AbstractThe gluconeogenic phosphoenolpyruvate (PEP) carboxykinase is active in Escherichia coli during its growth on glucose. The present study investigated the influence of growth rates and PEP carboxykinase knockout on the anaplerotic fluxes in E. coli. The intracellular fluxes were determined using the complementary methods of flux ratio analysis and metabolic flux analysis based on [U‐13C6]glucose labeling experiments and 2D nuclear magnetic resonance (NMR) spectroscopy of cellular amino acids and glycerol. Significant activity of PEP carboxykinase was identified in wild‐type E. coli, and the ATP dissipation for the futile cycling via this reaction accounted for up to 8.2% of the total energy flux. Flux analysis of pck deletion mutant revealed that abolishment of PEP carboxykinase activity resulted in a remarkably reduced flux through the anaplerotic PEP carboxylase and the activation of the glyoxylate shunt, with 23% of isocitrate found being channeled in the glyoxylate shunt. The changes in intracellular metabolite concentrations and specific enzyme activities associated with different growth rates and pck deletion, were also determined. Combining the measurement data of in vivo fluxes, metabolite concentrations and enzyme activities, the in vivo regulations of PEP carboxykinase flux, PEP carboxylation, and glyoxylate shunt in E. coli are discussed. © 2003 Wiley Periodicals, Inc. Biotechnol Bioeng 84: 129–144, 2003.
Stability of recombinant plasmids on the continuous culture of Bifidobacterium animalis ATCC 27536
Authors: González Vara Antonio , Rossi Maddalena , Altomare Luigi , Eikmanns Bernhard , Matteuzzi Diego 
Published: September 2003

AbstractBifidobacterium animalis ATCC 27536 represents among bifidobacteria a host‐model for cloning experiments. The segregational and structural stabilities of a family of cloning vectors with different molecular weights but sharing a common core were studied in continuous fermentation of the hosting B. animalis without selective pressure. The rate of plasmid loss (R) and the specific growth rate difference (δμ) between plasmid‐free and plasmid‐carrying cells were calculated for each plasmid and their relationship with plasmid size was studied. It was observed that both R and the numerical value of δμ increased exponentially with plasmid size. The exponential functions correlating the specific growth rate difference and the rate of plasmid loss with the plasmid molecular weight were determined. Furthermore, the smallest of the plasmids studied, pLAV (4.3‐kb) was thoroughly characterized by means of its complete nucleotide sequence. It was found that it contained an extra DNA fragment, the first bifidobacterial insertion sequence characterised, named IS 1999. © 2003 Wiley Periodicals, Inc. Biotechnol Bioeng 84: 145–150, 2003.
Binding and reversibility of Thermobifida fusca Cel5A, Cel6B, and Cel48A and their respective catalytic domains to bacterial microcrystalline cellulose
Authors: Jung Hyungil , Wilson David B. , Walker Larry P. 
Published: September 2003

AbstractThe binding and reversibility of Thermobifida fusca intact Cel5A, Cel5B, and Cel48A and their corresponding catalytic domains (CDs) to bacterial microcrystalline cellulose (BMCC) were studied at 5°C. The binding of the intact cellulases and of corresponding CDs to BMCC was irreversible in all regions: Langmuir binding (region I), interstice penetration (region II), and interstice saturation (region III). The three cellulose binding domains (CBMs) bind reversibly in “region I” although their respective CDs do not. The irreversible binding of these enzymes in the Langmuir region does not satisfy the Langmuir assumption; however, the overall fit of the Interstice Saturation model, which includes binding in MBCC interstices as well as on the freely accessible surface (Jung et al., 2002a) is good. The main limitation of the model is that it does not explicitly address a mechanism for forming the enzyme‐substrate complex within the active site of the CDs. © 2003 Wiley Periodicals, Inc. Biotechnol Bioeng 84: 151–159, 2003.
Simultaneous nitrification, denitrification, and phosphorus removal in a lab‐scale sequencing batch reactor
Authors: Zeng Raymond J. , Lemaire Romain , Yuan Zhiguo , Keller Jürg 
Published: September 2003

AbstractSimultaneous nitrification and denitrification (SND) via the nitrite pathway and anaerobic–anoxic‐enhanced biological phosphorus removal (EBPR) are two processes that can significantly reduce the energy and COD demand for nitrogen and phosphorus removal. The combination of these two processes has the potential of achieving simultaneous nitrogen and phosphorus removal with a minimal requirement for COD. A lab‐scale sequencing batch reactor (SBR) was operated in alternating anaerobic–aerobic mode with a low dissolved oxygen (DO) concentration (0.5 mg/L) during the aerobic period, and was demonstrated to accomplish nitrification, denitrification, and phosphorus removal. Under anaerobic conditions, COD was taken up and converted to polyhydroxyalkanoates (PHAs), accompanied by phosphorus release. In the subsequent aerobic stage, PHA was oxidized and phosphorus was taken up to <0.5 mg/L by the end of the cycle. Ammonia was also oxidized during the aerobic period, but without accumulation of nitrite or nitrate in the system, indicating the occurrence of simultaneous nitrification and denitrification. However, off‐gas analysis showed that the final denitrification product was mainly nitrous oxide (N2O), not N2. Further experimental results demonstrated that nitrogen removal was via nitrite, not nitrate. These experiments also showed that denitrifying glycogen‐accumulating organisms (DGAOs), rather than denitrifying polyphosphate‐accumulating organisms (DPAOs), were responsible for the denitrification activity. © 2003 Wiley Periodicals, Inc. Biotechnol Bioeng 84: 170–178, 2003.
Generic/matrix evaluation of SV40 clearance by anion exchange chromatography in flow‐through mode
Authors: Curtis Sherrie , Lee Kitty , Blank Gregory S. , Brorson Kurt , Xu Yuan 
Published: September 2003

AbstractThe potential of viral contamination is a regulatory concern for continuous cell line‐derived pharmaceutical proteins. Complementary and redundant safety steps, including an evaluation of the viral clearance capacity of unit operations in the purification process, are performed prior to registration and marketing of biotechnology pharmaceuticals. Because process refinement is frequently beneficial, CBER/FDA has published guidance facilitating process improvement by delineating specific instances where the bracketing and generic approaches are appropriate for virus removal validation. In this study, a generic/matrix study was performed using Q‐Sepharose Fast Flow (QSFF) chromatography to determine if bracketing and generic validation can be applied to anion exchange chromatography. Key operational parameters were varied to upper and lower extreme values and the impact on viral clearance was assessed using simian virus 40 (SV40) as the model virus. Operational ranges for key chromatography parameters were identified where an SV40 log10 reduction value (LRV) of ≥4.7 log10 is consistently achieved. On the basis of the apparent robustness of SV40 removal by Q‐anion exchange chromatography, we propose that the concept of “bracketed generic” validation can be applied to this and potentially other chromatography unit operations. © 2003 Wiley Periodicals, Inc. Biotechnol Bioeng 84: 179–186, 2003.
Kinetics of thermophilic, anaerobic oxidation of straight and branched chain butyrate and valerate
Authors: Batstone D. J. , Pind P. F. , Angelidaki I. 
Published: September 2003

AbstractThe degradation kinetics of normal and branched chain butyrate and valerate are important in protein‐fed anaerobic systems, as a number of amino acids degrade to these organic acids. Including activated and primary wastewater sludge digesters, the majority of full‐scale systems digest feeds with a significant or major fraction of COD as protein. This study assesses the validity of using a common kinetic parameter set and biological catalyst to represent butyrate, n‐valerate, and i‐valerate degradation in dynamic models. The i‐valerate degradation stoichiometry in a continuous, mixed population system is also addressed, extending previous pure‐culture and batch studies. A previously published mathematical model was modified to allow competitive uptake of i‐valerate, and used to model a thermophilic manure digester operated over 180 days. The digester was periodically pulsed with straight and branched chain butyrate and valerate. Parameters were separately optimized to describe butyrate, i‐valerate, and n‐valerate degradation, as well as a lumped set optimized for all three substrates, and nonlinear, correlated parameter spaces estimated using an F distribution in the objective function (J). Each parameter set occupied mutually exclusive parameter spaces, indicating that all were statistically different from each other. However, qualitatively, the influence on model outputs was similar, and the lumped set would be reasonable for mixed acid digestion. The main characteristic not represented by Monod kinetics was a delay in i‐valerate uptake, and was compensated for by a decreased maximum uptake rate (km). Therefore, the kinetics need modification if fed predominantly i‐valerate. Butyrate (i‐ and n‐) and n‐valerate could be modeled using stoichiometry consistent with β‐oxidation degradation pathways. However, i‐valerate produced acetate only, supporting the stoichiometry of a reaction determined by other researchers in pure culture. Therefore, lumping i‐valerate stoichiometry with that of n‐valerate will not allow good system representation, especially when the feed consists of proteins high in leucine (which produces i‐valerate), and the modified model structure and stoichiometry as proposed here should be used. This requires no additional kinetic parameters and one additional dynamic concentration state variable (i‐valerate) in addition to the variables in the base model. © 2003 Wiley Periodicals, Inc. Biotechnol Bioeng 84: 195–204, 2003.
Oscillating perfusion of cell suspensions through three‐dimensional scaffolds enhances cell seeding efficiency and uniformity
Authors: Wendt D. , Marsano A. , Jakob M. , Heberer M. , Martin I. 
Published: September 2003

AbstractWe developed a bioreactor for automated cell seeding of three‐dimensional scaffolds by continuous perfusion of a cell suspension through the scaffold pores in oscillating directions. Using quantitative biochemical and image analysis techniques, we then evaluated the efficiency and uniformity of perfusion seeding of Polyactive foams as compared to conventional static and spinner flask methods. Finally, we assessed the efficacy of the perfusion seeding technique for different scaffolds and cell types. Perfusion seeding of chondrocytes into Polyactive foams resulted in “viable cell seeding efficiencies,” defined as the percentages of initially loaded cells that were seeded and remained viable, that were significantly higher (75 ± 6%) than those by static (57% ± 5%) and spinner flask seeding (55% ± 8%). In addition, as compared to static and spinner flask methods, cells seeded by perfusion were respectively 2.6‐fold and 3.8‐fold more uniformly distributed and formed more homogeneously sized cell clusters. Chondrocytes seeded by perfusion into Hyaff®‐11 nonwoven meshes were 26% and 63%, respectively, more uniformly distributed than following static and spinner flask seeding. Bone marrow stromal cells seeded by perfusion into ChronOS™ porous ceramics were homogeneously distributed throughout the scaffold volume, while following the static method, cells were found only near the top surface of the ceramic. In summary, we demonstrated that our cell seeding perfusion bioreactor generated constructs with remarkably uniform cell distributions at high efficiencies, and was effective for a variety of scaffolds and different mesenchymal cell types. © 2003 Wiley Periodicals, Inc. Biotechnol Bioeng 84: 205–214, 2003.
Comparison of antibody functionality using different immobilization methods
Authors: Danczyk R. , Krieder B. , North A. , Webster T. , HogenEsch H. , Rundell A. 
Published: September 2003

AbstractThis study investigates the influence of antibody immobilization methods on antigen capture. Adsorption and two surface chemistries, an aminosilane chemistry and a common heterobifunctional crosslinker (N‐gamma‐maleimidobutyryloxy‐succinimide ester, GMBS), were compared and evaluated for their ability to immobilize antibodies and capture antigen. The role of protein A as an orienting protein scaffold component in each of these techniques was also evaluated. Through experimentation it was determined that the GMBS technique immobilized the highest amount of antibody and minimized nonspecific binding. For all techniques, the most functional antibodies were found to be those immobilized with protein A. Interestingly, the aminosilane technique demonstrated the highest antigen capture with antibody alone but also exhibited the highest level of nonspecific binding. © 2003 Wiley Periodicals. Biotechnol Bioeng 84: 215–223, 2003.
Tyrosinase: Polybrene noncovalent complexes in water‐ethanol mixtures
Authors: Shipovskov Stepan , Levashov Andrey 
Published: September 2003

AbstractFormation of noncovalent complexes between tyrosinase from mushrooms and a cationic polyelectrolyte, polybrene (PB, poly (1,5‐dimethyl‐1,5‐diazaundecamethyelene) bromide), was shown to activate and stabilize tyrosinase in water–ethanol mixtures. In the reaction of catechol oxidation in aqueous solutions, catalytic activity (kcat) of tyrosinase‐PB complex ([PB]/[tyrosinase] molar ratio 100:1, per mole of polymer) in a wide range of pH was higher than that of free tyrosinase. In aqueous solutions and in water–ethanol mixtures at moderate concentrations of ethanol (10–40% v/v), the value of kcat of tyrosinase‐PB complex exceeded the activity of free enzyme, from 1.2–2‐fold, accompanied by the essential (up to 10‐fold) increase in the value of the specificity constant (kcat/Km). The results are of practical importance for the construction of biocatalysts working successfully in polar organic media. © 2003 Wiley Periodicals, Inc. Biotechnol Bioeng 84 258–263, 2003.
Natural antimicrobial agent (reuterin) produced by lactobacillus reuteri for sanitization of biological tissues inoculated with pseudomonas aeruginosa
Authors: Liang Hsiang‐Fa , Chen Chiun‐Nan , Chang Yen , Sung Hsing‐Wen 
Published: September 2003

AbstractThe study was done to evaluate the efficacy of using reuterin produced by Lactobacillus reuteri to sanitize biological tissues. The microorganism tested in the study was Pseudomonas aeruginosa, a common cause of nosocomial biomaterial‐related infections. The inhibitory effect of reuterin on P. aeruginosa for an inoculated tissue was investigated at different conditions of concentration, temperature, and pH. Additionally, the cellular compatibility of the reuterin‐sanitized tissue was evaluated. Glutaraldehyde was employed as a control. It was noted that the minimum inhibitory concentration (MIC, 33.0 ± 2.9 ppm) and minimum bactericidal concentration (MBC, 50.0 ± 0.0 ppm) values of reuterin for P. aeruginosa were significantly lower than their glutaraldehyde counterparts (MIC, 130.0 ± 8.2 ppm and MBC, 180.0 ± 18.3 ppm). This indicated that reuterin was more efficient than glutaraldehyde as an antimicrobial agent. The addition of reuterin on the inoculated tissue led to a reduced viability of P. aeruginosa. The reduction in the P. aeruginosa culture was more pronounced with increasing the concentration of reuterin (0–100 ppm). At increasing temperature (25–45°C), there was an increasing effect of reuterin on its sanitization activity. However, it should be pointed out that the growth of P. aeruginosa in the nutrient broth was also significantly affected by temperature. The sanitization activity of reuterin was more evident with increasing the pH level (pH 6.5–8.5). The cytotoxicity of reuterin was significantly lower than that of glutaraldehyde. Additionally, the cellular compatibility of the reuterin‐sanitized tissue was superior to its glutaraldehyde‐sanitized counterpart. © 2003 Wiley Periodicals, Inc. Biotechnol Bioeng 84: 233–239, 2003.
Development of foamed emulsion bioreactor for air pollution control
Authors: Kan Eunsung , Deshusses Marc A. 
Published: September 2003

AbstractA new type of bioreactor for air pollution control has been developed. The new process relies on an organic‐phase emulsion and actively growing pollutant‐degrading microorganisms, made into a foam with the air being treated. This new reactor is referred to as a foamed emulsion bioreactor (FEBR). As there is no packing in the reactor, the FEBR is not subject to clogging. Mathematical modeling of the process and proof of concept using a laboratory prototype revealed that the foamed emulsion bioreactor greatly surpasses the performance of existing gas‐phase bioreactors. Experimental results showed a toluene elimination capacity as high as 285 gtoluene m−3reactor h−1 with a removal efficiency of 95% at a gas residence time of 15 s and a toluene inlet concentration of 1–1.3 g m−3. Oxygen limited the reactor performance at toluene concentration above about 0.7–1.0 g m−3; consequently, performance was significantly improved when pure oxygen was added to the contaminated air. The elimination capacity increased from 204 to 408 g m−3 h−1 with >77% toluene removal at toluene inlet concentrations of 2–2.2 g m−3. Overall, the results show that the performance of the FEBR far exceeds that of currently used bioreactors for air pollution control. © 2003 Wiley Periodicals, Inc. Biotechnol Bioeng 84: 240–244, 2003.
Synergistic cellulose hydrolysis can be described in terms of fractal‐like kinetics
Authors: Väljamäe Priit , Kipper Kalle , Pettersson Göran , Johansson Gunnar 
Published: September 2003

AbstractA fractal‐like kinetics model was used to describe the synergistic hydrolysis of bacterial cellulose by Trichoderma reesei cellulases. The synergistic action of intact cellobiohydrolase Cel7A and endoglucanase Cel5A at low enzyme‐to‐substrate ratios showed an apparent substrate inhibition consistent with a case where two‐dimensional (2‐D) surface diffusion of the cellobiohydrolase is rate‐limiting. The action of Cel7A core and Cel5A was instead consistent with a three‐dimensional (3‐D) diffusion‐based mode of action. The synergistic action of intact Cel7A was far superior to that of the core at a high enzyme‐to‐substrate ratio, but this effect was gradually reduced at lower enzyme‐to‐substrate ratios. The apparent fractal kinetics exponent h obtained by nonlinear fit of hydrolysis data to the fractal‐like kinetics analogue of a first‐order reaction was a useful empirical parameter for assessing the rate retardation and its dependence on the reaction conditions. © 2003 Wiley Periodicals, Inc. Biotechnol Bioeng 84: 254–257, 2003.