bluuebunny/crossref_metadata_2025_split huggingface dataset:
Responses of the photosynthetic machinery of Spirulina maxima to induced reactive oxygen species
Authors: Ganesh Aparna B. , Manoharan Periakaruppan T. , Suraishkumar G.K. 
Published: September 2006

AbstractThe photosynthetic machinery of Spirulina maxima was studied when subjected to induced reactive oxygen species (ROS) to examine the organism's responses to stress. Significant decreases in both photosynthetic efficiency and growth rate were observed. Exposure to 0.01 mmol H2O2/(g cell), which induced the lowest specific intracellular ROS level (siROS) led to a 15% decrease in specific growth rate; an increase in siROS by 70‐fold led to a 25% decrease in specific growth rate. Similarly, siROS induced by 0.01 mmol H2O2/(g cell) led to 15% inhibition in photosynthetic efficiency, while an increase in siROS by 40‐ or 70‐fold led to about 60% inhibition in photosynthetic efficiency. To further understand the effects of induced ROS on photosynthetic machinery, we performed a detailed pigmentation analysis as well as analyzed Phycobilisomes (PBS), Photosystem II (PSII), and Photosystem I (PSI), the three important components of cyanobacterial photosynthetic apparatus. We found carotenoids (beta‐carotene and lutein) to be most sensitive to siROS. Also, specific levels of phycocyanin and allophycocyanin, which are important PBS pigments, decreased significantly in response to H2O2. Further, electron transport assays revealed that ROS cause damage primarily to PSII, whereas they do not significantly affect PSI in comparison; siROS induced by 0.01 mmol H2O2/(g cell) led to a 15% inhibition of PSII, and increase in siROS by 9‐, 40‐, and 70‐fold led to 22%, 36%, and 46% inhibition, respectively. Biotechnol. Bioeng. 2007;96:1191–1198. © 2006 Wiley Periodicals, Inc.
The conformational quality of insoluble recombinant proteins is enhanced at low growth temperatures
Authors: Vera Andrea , González‐Montalbán Nuria , Arís Anna , Villaverde Antonio 
Published: September 2006

AbstractProtein aggregation is a major bottleneck during the bacterial production of recombinant proteins. In general, the induction of gene expression at sub‐optimal growth temperatures improves the solubility of aggregation‐prone polypeptides and minimizes inclusion body (IB) formation. However, the effect of low temperatures on the quality of the recombinant protein, especially within the insoluble cell fraction, has been hardly ever explored. In this work, we have examined the conformational status of a recombinant GFP protein when produced in Escherichia coli below 37°C. As expected, the fraction of aggregated protein largely decreased at lower temperatures, while the conformational quality of both soluble and aggregated GFP, as reflected by its specific fluorescence emission, progressively improved. This observation indicates that physicochemical conditions governing protein folding affect concurrently the quality of the soluble and the aggregated forms of a misfolding‐prone protein, and that protein misfolding and aggregation are clearly not coincident events. Biotechnol. Bioeng. 2007;96:1101–1106. © 2006 Wiley Periodicals, Inc.
The YfiD protein contributes to the pyruvate formate‐lyase flux in an Escherichia coli arcA mutant strain
Authors: Zhu Jiangfeng , Shalel‐Levanon Sagit , Bennett George , San Ka‐Yiu 
Published: September 2006

AbstractThe product of yfiD gene is similar to pyruvate formate‐lyase (PFL) activase and it has been reported to activate PFL by replacing the glycyl radical domain. To quantitate the effect of YfiD on the cell metabolism in microaerobic cultures, glucose‐limited chemostat cultures were conducted with Escherichia coli yfiD mutant and yfiDarcA mutant strains. The microaerobic condition was controlled by purging the culture media with 2.5% O2 in N2. The intracellular metabolic flux distributions in these cultures were estimated based on C‐13 labeling experiments. By comparing with the flux distributions in wild‐type E. coli and the arcA mutant, it was shown that YfiD contributes to about 18% of the PFL flux in the arcA mutant, but it did not contribute to the PFL flux in wild‐type E. coli. It was also shown that the cell used both PFL and pyruvate dehydrogenase (PDH) to supplement the acetyl‐coenzyme A (AcCoA) pool under microaerobic conditions. The flux through PDH was about 22–30% of the total flux toward AcCoA in the wild‐type, the yfiD mutant and yfiDarcA mutant strains. Relatively higher lactate production was seen in the yfiDarcA mutant than the other strains, which was due to the lower total flux through PFL and PDH toward AcCoA in this strain. Biotechnol. Bioeng. 2007;97:138–143. © 2006 Wiley Periodicals, Inc.
Production of bio‐hydrogen by mesophilic anaerobic fermentation in an acid‐phase sequencing batch reactor
Authors: Cheong Dae‐Yeol , Hansen Conly L. , Stevens David K. 
Published: September 2006

AbstractThe pH and hydraulic retention time (HRT) of an anaerobic sequencing batch reactor (ASBR) were varied to optimize the conversion of carbohydrate‐rich synthetic wastewater into bio‐hydrogen. A full factorial design using evolutionary operation (EVOP) was used to determine the effect of the factors and to find the optimum condition of each factor required for high hydrogen production rate. Experimental results from 20 runs indicate that a maximum hydrogen production rate of 4,460–5,540 mL/L/day under the volumetric organic loading rate (VOLR) of 75 g‐COD/L/day obtained at an observed design point of HRT = 8 h and pH = 5.7. The hydrogen production rate was strongly dependent on the HRT, and the effect was statistically significant (P < 0.05). However, no significant effect (P > 0.05) was found for the pH on the hydrogen production rate. When the ASBR conditions were set for a maximum hydrogen production rate, the hydrogen production yield and specific hydrogen production rate were 60–74 mL/g‐COD and 330–360 mL/g‐VSS/day, respectively. The hydrogen composition was 43–51%, and no methanogenesis was observed. Acetate, propionate, butyrate, valerate, caproate, and ethanol were major liquid intermediate metabolites during runs of this ASBR. The dominant fermentative types were butyrate‐acetate or ethanol‐acetate, representing the typical anaerobic pathway of Clostridium species. This hydrogen‐producing ASBR had a higher hydrogen production rate, compared with that produced using continuous‐flow stirred tank reactors (CSTRs). This study suggests that the hydrogen‐producing ASBR is a promising bio‐system for prolonged and stable hydrogen production. Biotechnol. Bioeng. 2007;96: 421–432. © 2006 Wiley Periodicals, Inc.
Gastroesophageal reflux symptoms in patients with adenocarcinoma of the esophagus or cardia
Authors: Chak Amitabh , Faulx Ashley , Eng Charis , Grady William , Kinnard Margaret , Ochs‐Balcom Heather , Falk Gary 
Published: October 2006

AbstractBACKGROUND.The efficacy of endoscopic screening for chronic gastroesophageal reflux symptoms of heartburn and regurgitation in adult subjects depends on the sensitivity of this strategy for detecting Barrett esophagus in subjects before the development of adenocarcinoma of the esophagus or cardia. The aim of the current study was to determine what proportion of patients with cancer of the esophagus or cardia would have been candidates for a screening endoscopy before their cancer diagnosis based on the presence and duration of preceding reflux symptoms.METHODS.All patients with adenocarcinoma of the esophagus, adenocarcinoma of the cardia, or long‐segment Barrett esophagus presenting for endoscopy at 4 tertiary care and 2 Veterans Affairs (VA) hospitals were given a previously validated questionnaire to determine their recall of common gastroesophageal reflux symptoms.RESULTS.The study population of 375 subjects consisted primarily of 294 (78%) white men. Only 67 of 110 patients (61%) with adenocarcinoma of the esophagus and 8 of 21 patients (38%) with adenocarcinoma of the cardia recalled symptoms of heartburn or regurgitation being present for >5 years before their diagnosis of cancer. Only 40 of 110 patients (36%) with adenocarcinoma of the esophagus and 5 of 21 patients (24%) with adenocarcinoma of the cardia recalled weekly symptoms being present for >5 years before their cancer diagnosis. Of the 244 patients with Barrett esophagus, 170 (70%) recalled heartburn or regurgitation for >5 years and 89 patients (37%) recalled weekly symptoms for >5 years.CONCLUSIONS.Current practice, which uses a screening strategy of performing endoscopy in patients with >5 years of heartburn or regurgitation, can detect Barrett epithelium in only a limited proportion of those patients at risk for developing adenocarcinoma of the esophagus or adenocarcinoma of the cardia. Cancer 2006. © 2006 American Cancer Society.
The use of multivariate statistics to elucidate patterns of floodplain sedimentation at different spatial scales
Authors: Thoms Martin C. , Parsons Melissa E. , Foster John M. 
Published: October 2006

AbstractFloodplains are depositional features of riverine landscapes that display complex sedimentation patterns that are amenable to multi‐scale approaches. We examined sedimentation in the Lower Balonne floodplain, Queensland, Australia, at three different spatial scales: the channel (103 km), floodplain process zone (10 km) and geomorphic unit (102 m) scales, and compared scale‐related patterns evident from stratigraphy with those evident from quantitative multivariate analysis. Three stratigraphic sequences were found in the Lower Balonne floodplain: generally fining upward, episodic fining upward, and mud‐dominated. Stratigraphical analysis revealed the detailed character of sedimentary sequences embedded within the scale patterns derived from multivariate analysis. Multivariate statistical analyses of a range of textural and geochemical data revealed different patterns of floodplain sedimentation at each scale. At the channel scale, sediment texture and geochemistry were more heterogeneous in the Culgoa River than in Briarie Creek. At the floodplain process zone scale clear patterns of sediment texture and geochemistry were observed along the upper, mid and lower floodplain process zones of Briarie Creek, but not along the Culgoa River. At the geomorphic unit scale, clear patterns of sediment texture and geochemistry were observed among the bank, buried channel and flat floodplain units of the Culgoa River, but were not as clear in Briarie Creek. Recognition of rivers as hierarchically organized systems is an emerging paradigm in river science. Our study supports this paradigm by demonstrating that different sedimentation patterns occur at different scales to reveal a hierarchically organized floodplain environment. Copyright © 2006 John Wiley & Sons, Ltd.
Dating young geomorphic surfaces using age of colonizing Douglas fir in southwestern Washington and northwestern Oregon, USA
Authors: Pierson Thomas C. 
Published: October 2006

AbstractDating of dynamic, young (<500 years) geomorphic landforms, particularly volcanofluvial features, requires higher precision than is possible with radiocarbon dating. Minimum ages of recently created landforms have long been obtained from tree‐ring ages of the oldest trees growing on new surfaces. But to estimate the year of landform creation requires that two time corrections be added to tree ages obtained from increment cores: (1) the time interval between stabilization of the new landform surface and germination of the sampled trees (germination lag time or GLT); and (2) the interval between seedling germination and growth to sampling height, if the trees are not cored at ground level. The sum of these two time intervals is the colonization time gap (CTG). Such time corrections have been needed for more precise dating of terraces and floodplains in lowland river valleys in the Cascade Range, where significant eruption‐induced lateral shifting and vertical aggradation of channels can occur over years to decades, and where timing of such geomorphic changes can be critical to emergency planning.Earliest colonizing Douglas fir (Pseudotsuga menziesii) were sampled for tree‐ring dating at eight sites on lowland (<750 m a.s.l.), recently formed surfaces of known age near three Cascade volcanoes – Mount Rainier, Mount St. Helens and Mount Hood – in southwestern Washington and northwestern Oregon. Increment cores or stem sections were taken at breast height and, where possible, at ground level from the largest, oldest‐looking trees at each study site. At least ten trees were sampled at each site unless the total of early colonizers was less. Results indicate that a correction of four years should be used for GLT and 10 years for CTG if the single largest (and presumed oldest) Douglas fir growing on a surface of unknown age is sampled. This approach would have a potential error of up to 20 years. Error can be reduced by sampling the five largest Douglas fir instead of the single largest. A GLT correction of 5 years should be added to the mean ring‐count age of the five largest trees growing on the surface being dated, if the trees are cored at ground level. This correction would have an approximate error of ±5 years. If the trees are cored at about 1·4 m above the ground surface (breast height), a CTG correction of 11 years should be added to the mean age of the five sampled trees (with an error of about ±7 years). Published in 2006 by John Wiley & Sons, Ltd.
Cancer‐germline gene expression in pediatric solid tumors using quantitative real‐time PCR
Authors: Jacobs Joannes F.M. , Brasseur Francis , Hulsbergen‐van de Kaa Christina A. , van de Rakt Mandy W.M.M. , Figdor Carl G. , Adema Gosse J. , Hoogerbrugge Peter M. , Coulie Pierre G. , de Vries I. Jolanda M. 
Published: October 2006

AbstractCancer‐germline genes (CGGs) code for immunogenic antigens that are present on various human tumors but not on normal tissues. The importance of CGGs in cancer immunotherapy has led to detailed studies of their expression in a range of human tumors. We measured the levels of expression of 12 CGGs in various pediatric solid tumors to identify targets for therapeutic cancer vaccines. Quantitative real‐time PCR (qPCR) was used to measure the expression of 8 MAGE genes and of genes LAGE‐2/NY‐ESO‐1 and GAGE‐1, 2, 8 in 9 osteosarcomas, 10 neuroblastomas, 12 rhabdomyosarcomas and 18 Ewing's sarcomas. Nine tumors were also examined by immunohistochemistry with monoclonal antibodies specific for the MAGE‐A1, MAGE‐A4 and NY‐ESO‐1 proteins. All osteosarcoma and 80% of neuroblastoma samples expressed several CGGs at high levels. Six of 12 rhabdomyosarcomas and 11 of 18 Ewing's sarcomas expressed at least one CGG. Immunohistochemistry data correlated well with qPCR results and showed a homogeneous protein distribution pattern in most positive tumors. No correlation was found between the levels of CGG expression in the tumors and clinicopathological parameters of the patients. Pediatric solid tumors express several CGGs, which encode antigens that could be targeted in therapeutic vaccination trials. Several CGGs of the MAGE, GAGE and LAGE families are coexpressed in a large proportion of osteosarcoma and neuroblastoma samples. Some rhabdomyosarcomas express several of these genes at high levels. Ewing's sarcomas have an overall low CGG expression. © 2006 Wiley‐Liss, Inc.
Comparison of implicit solvent models for the simulation of protein–surface interactions
Authors: Sun Yu , Latour Robert A. 
Published: October 2006

AbstractEmpirical force field‐based molecular simulations can provide valuable atomistic‐level insights into protein–surface interactions in aqueous solution. While the implicit treatment of solvation effects is desired as a means of improving simulation efficiency, existing implicit solvent models were primarily developed for the simulation of peptide or protein behavior in solution alone, and thus may not be appropriate for protein interactions with synthetic material surfaces. The objective of this research was to calculate the change in free energy as a function of surface–separation distance for peptide–surface interactions using different empirical force field‐based implicit solvation models (ACE, ASP, EEF1, and RDIE with the CHARMM 19 force field), and to compare these results with the same calculations conducted using density functional theory (DFT) combined with the self‐consistent reaction field (SCRF) implicit solvation model. These comparisons show that distinctly different types of behavior are predicted with each implicit solvation method, with ACE providing the best overall agreement with DFT/SCRF calculations. These results also identify areas where ACE is in need of improvement for this application and provide a basis for subsequent parameter refinement. © 2006 Wiley Periodicals, Inc. J Comput Chem, 2006
Reflections on migration of clay and structural changes in nanocomposites
Authors: Lewin Menachem 
Published: October 2006

AbstractThe profound effect on flame retardancy of the blending of small amounts of clay with polymers is believed to be due to the formation of a protective clay‐rich char barrier on the surface of the pyrolyzing polymer during combustion. The mode of formation of this barrier is discussed, in view of recent results. Evidence is reviewed, showing that the organically layered silicon particles migrate to, and accumulate on the surface of the molten polymer at temperatures far below pyrolysis temperature. The causes of the migration are: temperature and viscosity gradients of the melt with regard to heat source; propelling the organically layered silicon to the surface by gas bubbles from the decomposing surfactant and polymer; and by the difference in surface free energy between the polymer and the polymer/clay aggregate. The interfacial tension of the clay/polymer aggregates is calculated for a number of polymers, and shown to be much lower than the surface tension of the low surface free energy ingredient. It is suggested that these aggregates migrate to the surface. The decomposition of the surfactant in the clay above 200°C brings about, in the case of polypropylene/nanocomposite, two simultaneous and opposing phenomena: the migration of the clay; and the conversion of the nanocomposite into a non‐colloidal microcomposite. The decomposition of the surfactant is accompanied by an increase in interlayer distance, and internal pressure in the clay particles, culminating either in a separation of the external layers (i.e. exfoliation), or in their collapse into each other, forming a microcomposite. Mechanistic considerations are presented. Copyright © 2006 John Wiley & Sons, Ltd.
Electroactive composite systems containing high conductive polymer layers on poly(ethylene) porous films
Authors: Elyashevich G. K. , Smirnov M. A. , Kuryndin I. S. , Bukošek V. 
Published: October 2006

AbstractNew composite electroactive materials containing conducting polymers were elaborated by oxidative polymerization of aniline and pyrrole onto porous poly(ethylene) films. The morphology of the conducting phase on the surface of the composites was investigated by scanning electron microscopy. The influence of preparation method and porous support structure on electric and mechanical properties of the composite materials was studied. The correlation between the composites electroconductivity and the absorbance of electromagnetic radiation in the IR region was observed. It was found that gas separation and ion‐exchange membrane properties of the composites strongly depend on their conductivity and content of conducting component. Copyright © 2006 John Wiley & Sons, Ltd.
Unambiguous identification of thiouracil residue in urine collected in non‐treated bovine by tandem and high‐resolution mass spectrometry
Authors: Pinel Gaud , Maume Daniel , Deceuninck Yoann , Andre François , Le Bizec Bruno 
Published: October 2006

AbstractThyrostats are banned compounds in Europe since 1981 (directive 81/602/EC) because of their carcinogenic and teratogenic properties. However, the occurrence of thiouracil (TU) in bovine urines from national monitoring plans with quantifications in the range 1–10 µg · L−1 occasionally raises the question of its origin which might either be the consequence of an illegal administration or the result of ‘endogenous’ production. In order to definitively and unambiguously identify the so‐called thiouracil signal in non‐treated bovine urines, independent mass spectrometry (MS) approaches have been used. Different reagents (3‐IBBr, 3‐BrBBr and PFBBr) were used to derivatise and to extract TU from urine samples and characterisation of the residues was performed by means of different MS approaches [LC/(ESI‐)MS/MS, GC/(EI+)MS/MS and HRMS (EI and NCI)]. These combined strategies allowed for an independent and confident identification of TU in bovine urine samples collected from animals never treated with any thyrostatic drugs. This result is of prime importance for laboratories and risk managers involved in the field of forbidden growth promoters control: detection of TU residue in bovine urine will have to be carefully considered as a non‐systematic proof of illegal administration. Copyright © 2006 John Wiley & Sons, Ltd.
An adaptive phase I design for identifying a biologically optimal dose for dual agent drug combinations
Authors: Mandrekar Sumithra J. , Cui Yue , Sargent Daniel J. 
Published: October 2006

AbstractHistorically, designs for dose seeking trials using chemotherapeutic drug combinations have been geared towards finding the maximum tolerated dose, with safety as the primary outcome. With target based agents whose dose–efficacy curves are unknown and dose–toxicity relationships may be minimal, alternative designs are needed. In this paper, we propose an extension to an adaptive single agent dose‐finding design previously reported. A generalization of the continuation ratio model allowing separate toxicity and efficacy curves for each agent in a dual agent combination, generating a dose success surface for the combination, is proposed. A continual reassessment approach with a straightforward dose selection criterion using the accumulated data from all patients treated to that point is employed. Our simulation studies demonstrate favourable operating characteristics in terms of experimentation and recommendation rates, and the average sample size, under a variety of scenarios. The proposed approach allowing the incorporation of both the toxicity and efficacy of each agent into the identification of an optimal dosing region for a combination is novel and warrants further consideration. Copyright © 2006 John Wiley & Sons, Ltd.