bluuebunny/crossref_metadata_2025_split huggingface dataset:
Hierarchical amino acid utilization and its influence on fermentation dynamics: rifamycin B fermentation using Amycolatopsis mediterraneiS699, a case study
Authors: Bapat Prashant M , Das Debasish , Sohoni Sujata V , Wangikar Pramod P 
Published: November 2006

Abstract

Background
Industrial fermentation typically uses complex nitrogen substrates which consist of mixture of amino acids. The uptake of amino acids is known to be mediated by several amino acid transporters with certain preferences. However, models to predict this preferential uptake are not available. We present the stoichiometry for the utilization of amino acids as a sole carbon and nitrogen substrate or along with glucose as an additional carbon source. In the former case, the excess nitrogen provided by the amino acids is excreted by the organism in the form of ammonia. We have developed a cybernetic model to predict the sequence and kinetics of uptake of amino acids. The model is based on the assumption that the growth on a specific substrate is dependent on key enzyme(s) responsible for the uptake and assimilation of the substrates. These enzymes may be regulated by mechanisms of nitrogen catabolite repression. The model hypothesizes that the organism is an optimal strategist and invests resources for the uptake of a substrate that are proportional to the returns.

Results
Stoichiometric coefficients and kinetic parameters of the model were estimated experimentally for Amycolatopsis mediterranei S699, a rifamycin B overproducer. The model was then used to predict the uptake kinetics in a medium containing cas amino acids. In contrast to the other amino acids, the uptake of proline was not affected by the carbon or nitrogen catabolite repression in this strain. The model accurately predicted simultaneous uptake of amino acids at low cas concentrations and sequential uptake at high cas concentrations. The simulated profile of the key enzymes implies the presence of specific transporters for small groups of amino acids.

Conclusion
The work demonstrates utility of the cybernetic model in predicting the sequence and kinetics of amino acid uptake in a case study involving Amycolatopsis mediterranei, an industrially important organism. This work also throws some light on amino acid transporters and their regulation in A. mediterranei .Further, cybernetic model based experimental strategy unravels formation and utilization of ammonia as well as its inhibitory role during amino acid uptake. Our results have implications for model based optimization and monitoring of other industrial fermentation processes involving complex nitrogen substrate.
Pathway-specific differences between tumor cell lines and normal and tumor tissue cells
Authors: Ertel Adam , Verghese Arun , Byers Stephen W , Ochs Michael , Tozeren Aydin 
Published: November 2006

Abstract

Background
Cell lines are used in experimental investigation of cancer but their capacity to represent tumor cells has yet to be quantified. The aim of the study was to identify significant alterations in pathway usage in cell lines in comparison with normal and tumor tissue.

Methods
This study utilized a pathway-specific enrichment analysis of publicly accessible microarray data and quantified the gene expression differences between cell lines, tumor, and normal tissue cells for six different tissue types. KEGG pathways that are significantly different between cell lines and tumors, cell lines and normal tissues and tumor and normal tissue were identified through enrichment tests on gene lists obtained using Significance Analysis of Microarrays (SAM).

Results
Cellular pathways that were significantly upregulated in cell lines compared to tumor cells and normal cells of the same tissue type included ATP synthesis, cell communication, cell cycle, oxidative phosphorylation, purine, pyrimidine and pyruvate metabolism, and proteasome. Results on metabolic pathways suggested an increase in the velocity nucleotide metabolism and RNA production. Pathways that were downregulated in cell lines compared to tumor and normal tissue included cell communication, cell adhesion molecules (CAMs), and ECM-receptor interaction. Only a fraction of the significantly altered genes in tumor-to-normal comparison had similar expressions in cancer cell lines and tumor cells. These genes were tissue-specific and were distributed sparsely among multiple pathways.

Conclusion
Significantly altered genes in tumors compared to normal tissue were largely tissue specific. Among these genes downregulation was a major trend. In contrast, cell lines contained large sets of significantly upregulated genes that were common to multiple tissue types. Pathway upregulation in cell lines was most pronounced over metabolic pathways including cell nucleotide metabolism and oxidative phosphorylation. Signaling pathways involved in adhesion and communication of cultured cancer cells were downregulated. The three way pathways comparison presented in this study brings light into the differences in the use of cellular pathways by tumor cells and cancer cell lines.
Reduction of nosocomial pneumonia after major burns by trace element supplementation: aggregation of two randomised trials
Authors: Berger Mette M , Eggimann Philippe , Heyland Daren K , Chioléro René L , Revelly Jean-Pierre , Day Andrew , Raffoul Wassim , Shenkin Alan 
Published: November 2006

Abstract
Introduction
Nosocomial pneumonia is a major source of morbidity and mortality after severe burns. Burned patients suffer trace element deficiencies and depressed antioxidant and immune defences. This study aimed at determining the effect of trace element supplementation on nosocomial or intensive care unit (ICU)-acquired pneumonia.

Methods
Two consecutive, randomised, double-blinded, supplementation studies including two homogeneous groups of 41 severely burned patients (20 placebo and 21 intervention) admitted to the burn centre of a university hospital were combined. Intervention consisted of intravenous trace element supplements (copper 2.5 to 3.1 mg/day, selenium 315 to 380 μg/day, and zinc 26.2 to 31.4 mg/day) for 8 to 21 days versus placebo. Endpoints were infections during the first 30 days (predefined criteria for pneumonia, bacteraemia, wound, urine, and other), wound healing, and length of ICU stay. Plasma and skin (study 2) concentrations of selenium and zinc were determined on days 3, 10, and 20.

Results
The patients, 42 ± 15 years old, were burned on 46% ± 19% of body surface: the combined characteristics of the patients did not differ between the groups. Plasma trace element concentrations and antioxidative capacity were significantly enhanced with normalisation of plasma selenium, zinc, and glutathione peroxidase concentrations in plasma and skin in the trace element-supplemented group. A significant reduction in number of infections was observed in the supplemented patients, which decreased from 3.5 ± 1.2 to 2.0 ± 1.0 episodes per patient in placebo group (p < 0.001). This was related to a reduction of nosocomial pneumonia, which occurred in 16 (80%) patients versus seven (33%) patients, respectively (p < 0.001), and of ventilator-associated pneumonia from 13 to six episodes, respectively (p = 0.023).

Conclusion
Enhancing trace element status and antioxidant defences by selenium, zinc, and copper supplementation was associated with a decrease of nosocomial pneumonia in critically ill, severely burned patients.
What I Think I May Have Learned—Reflections on 50 Years of Teaching: An Interview with Michael Wertheimer
Authors: Michael Kurt D. 
Published: November 2006

Kurt Michael is an associate professor in the Department of Psychology at Appalachian State University (ASU) where he teaches history and systems of psychology, abnormal psychology, child psychopathology, and interventions for children and adolescents. He received his BA (cum laude) from the University of Colorado at Boulder and his MS and PhD in clinical psychology from Utah State University. He completed his internship in clinical psychology at Duke University Medical Center. His empirical research has focused on the assessment and treatment of child and adolescent psychopathology, meta-analytic designs, and the efficacy of brief interventions for excessive alcohol consumption among college students. In addition to his teaching and research endeavors, he serves as associate director for Clinical Services at ASU's Institute for Health and Human Services. Michael Wertheimer, professor emeritus at the University of Colorado at Boulder, has won awards for the teaching of psychology, for service, and for contributions to the history of psychology. After earning his BA (with high honors) from Swarthmore College and an MA in psychology from The Johns Hopkins University, he received his PhD in experimental psychology from Harvard University under the supervision of S. S. Stevens and Edwin G. Boring. He also worked for 1 semester as a full-time research assistant to social psychologist Solomon E. Asch. His career at the University of Colorado at Boulder (after teaching for 3 years at Wesleyan University) included decades of service as director or codirector of the departmental honors program in psychology (1956 to 1993) as well as the presidency of Divisions 1 (General), 2 (Society for the Teaching of Psychology), 24 (Theoretical and Philosophical Psychology—twice), and 26 (History) of the American Psychological Association (APA) and of Psi Chi and the Rocky Mountain Psychological Association. Among his scholarly endeavors in the history of psychology is the preservation of his father's (Max Wertheimer) contributions to the development of Gestalt theory (King & Wertheimer, 2005). He is the recipient of the Distinguished Teaching Award of the American Psychological Foundation and a Lifetime Achievement Award for Sustained, Outstanding, and Unusual Contributions to the History of Psychology from the APA's Division 26.
Bounds and Approximations for the Fixed-Cycle Traffic-Light Queue
Authors: van den Broek M. S. , van Leeuwaarden J. S. H. , Adan I. J. B. F. , Boxma O. J. 
Published: November 2006

This paper deals with the fixed-cycle traffic-light (FCTL) queue, where vehicles arrive at an intersection controlled by a traffic light and form a queue. The traffic light alternates between green and red periods, and delayed vehicles are assumed to depart during the green period at equal time intervals. The key performance characteristic in the FCTL queue is the so-called mean overflow, defined as the mean queue length at the end of a green period.An exact solution for the mean overflow is available, but it has been considered to be of little practical value because it requires some numerical procedures. Therefore, most of the literature on the FCTL queue is about deriving approximations for the mean overflow. In deriving these approximations, most authors first approximate the FCTL queue by a bulk-service queue, approximate the mean overflow in the bulk-service queue, and use this as an approximation for the mean overflow in the FCTL queue. So far no quantitative comparison of both models has been given. We compare both models and assess the quality of the approximation for various settings of the parameter values. In this comparison and throughout the paper we do not restrict ourselves to Poisson arrivals, but consider a more general arrival process instead.We discuss the numerical issues that need to be resolved to calculate the exact expression for the mean overflow in both queues and show that clear computational schemes are available. Next, we present several bounds and approximations of the mean overflow that do not require numerical procedures. In particular, we derive a new approximation based on the heavy traffic limit and a scaling argument. We compare the new bounds and approximation with the existing ones. We elaborate on the impact of several parameters, like the length of the green and red period and the variance of the arrival distribution. Each of these parameters turns out to be crucial.
First identification of a phosphorylcholine-substituted protein from Caenorhabditis elegans: isolation and characterization of the aspartyl protease ASP-6
Authors: Lochnit Günter , Grabitzki Julia , Henkel Björn , Tavernarakis Nektarios , Geyer Rudolf 
Published: November 2006

AbstractCaenorhabditis elegansis a widely accepted model system for parasitic nematodes, drug screening and developmental studies. Similar to parasitic worms,C. elegansexpresses glycosphingolipids and glycoproteins carrying, in part, phosphorylcholine (PCho) substitutions, which might play important roles in nematode development, fertility and, at least in the case of parasites, survival within the host. With the exception of a major secretory/excretory product fromAcanthocheilonema viteae(ES-62), no protein carrying this epitope has been studied in detail yet. Here we report on the identification, characterization and localization of the aspartyl protease ASP-6 ofC. elegans, which is excreted by the nematode in aPCho-substituted form. Within the worm, most prominent expression of the protein is observed in the intestine, while muscle and epithelial cells expressasp-6to a lesser extent. In animals harboring an ASP-6::GFP fusion protein, diffuse fluorescence throughout the body cavity of adult worms indicates that the chimeric protein is secreted.
RE1 Silencing Transcription Factor Maintains a Repressive Chromatin Environment in Embryonic Hippocampal Neural Stem Cells
Authors: Greenway Deborah J. , Street Miyoko , Jeffries Aaron , Buckley Noel J. 
Published: November 2006

Abstract
The control of gene expression in neural stem cells is key to understanding their developmental and therapeutic potential, yet we know little of the transcriptional mechanisms that underlie their differentiation. Recent evidence has implicated the RE1 silencing transcription factor (REST) in neuronal differentiation. However, the means by which REST regulates transcription in neural stem cells remain unclear. Here, we show that REST recruits distinct corepressor platforms in neural stem cells. REST is able to both silence and repress neuronal genes in embryonic hippocampal neural stem cells by creating a chromatin environment that contains both repressive local epigenetic signature (characterized by low levels of histones H4 and H3K9 acetylation and elevated dimethylation of H3K9) and H3K4 methylation, which are characteristic of gene activation. Furthermore, inhibition of REST function leads to activation of several neuron-specific genes but does not lead to overt formation of mature neurons, supporting the notion that REST regulates part, but not all, of the neuronal differentiation program.
Caged Molecules: Principles and Practical Considerations
Authors: Kao Joseph P.Y. 
Published: November 2006

AbstractA caged molecule is an inert but photosensitive molecule that is transformed by photolysis into a biologically active molecule at high speed (typically 1 msec). The process is referred to as photorelease. The spatial resolution of photorelease is limited by the properties of light; submicrometer resolution is potentially achievable. Therefore, focal photorelease of caged molecules enables one to control biological processes with high spatio‐temporal precision. The principles underlying caged molecules as well as practical considerations for their use are discussed in this unit.
Optimizing Laser Source Operation for Confocal and Multiphoton Laser Scanning Microscopy
Authors: McConnell Gail 
Published: November 2006

AbstractConfocal laser scanning microscopy (CLSM) and multiphoton laser scanning microscopy (MPLSM) are methods both widely used by life‐sciences researchers for imaging fluorescently labeled live cells and fixed tissue specimens. Key to the success of both CLSM and MPLSM is the application of a suitable laser source, namely one that provides sufficient average or peak power at the correct wavelength to excite fluorescence. High stability of the laser source output is required for three‐dimensional imaging, time‐lapse studies of live cells, and quantitative studies and inter‐experiment comparisons. The laser technology associated with the design of such lasers is mature, yet is unfortunately rather complex. This complexity can be off‐putting for the life‐sciences researcher who needs to optimize the system for the best possible images, but this apprehension can be overcome by understanding the function of the system components. This unit summarizes the optimization of the most commonly used laser sources for CLSM and MPLSM, including power and wavelength tuning and methods for cleaning optical components.
Model‐based optimization of feeding recipe for rifamycin fermentation
Authors: Bapat Prashant M. , Padiyar Nitin U. , Dave Nishant N. , Bhartiya Sharad , Wangikar Pramod P. , Dash Sachi 
Published: November 2006

AbstractIndustrial fermentation processes typically use complex media and operate in fed‐batch mode to minimize the effects of catabolite repression. However, model‐based feeding recipes have not been reported for such processes primarily as a result of the lack of reliable process models. By using a recently published process model, we optimize the feeding recipe for rifamycin B fermentation in complex media. Experimental validation shows a twofold improvement in productivity over an optimized batch. The dynamic optimization problem was posed as a nonlinear program and solved using successive quadratic programming. The feed profiles of four substrates were parameterized to convert the problem into a finite decision space consisting of substrate feed rates and switching intervals. Several distinct recipes, each corresponding to a unique initial guess of decision variables, showed comparable productivity, implying the presence of multiple local optima. The strategy presented here can be applied for optimization of other fermentation processes for which reliable process models are available. © 2006 American Institute of Chemical Engineers Engineers AIChE J, 2006
Measurements of skin surface temperature during mobile phone use
Authors: Anderson V. , Rowley J. 
Published: November 2006

AbstractWe measured maximum temperature rises on the side of the face after 6 min of continuous mobile phone operation using two models of AMPS analog phones operating in the 835 MHz band and three early model GSM digital phones operating in the 900 MHz band. For the GSM phones the highest recorded temperature rise difference was 2.3 °C and for the AMPS phones it was 4.5 °C, both at locations on the cheek. The higher differential temperature rise between AMPS and GSM may reflect the higher maximum average operating power of AMPS (600 mW) versus GSM900 (250 mW). Additionally, we compared temperature changes at a consistent location on the cheek for an AMPS phone that was inoperative (−0.7 °C), transmitting at full power (+2.6 °C) and in stand‐by mode (+2.0 °C). Our results suggest that direct RF heating of the skin only contributes a small part of the temperature rise and that most is due to heat conduction from the handset. Bioelectromagnetics 2007. © 2006 Wiley‐Liss, Inc.
A new technique to anchor stents for exact placement in ostial stenoses: The stent tail wire or Szabo technique
Authors: Kern Morton J. , Ouellette David , Frianeza Tony 
Published: November 2006

AbstractThis report describes a technique for correct positioning of a stent in an ostial stenosis by using a second wire passed through the last cell of a stent. The anchor wire technique, first described by Szabo et al. [Szabo S, Abramowitz B, Vaitkus PT. Am J Cardiol 2005;96:212H], will facilitate precise ostial stent placement and eliminate errors of positioning inside or outside the ostial narrowing. © 2006 Wiley‐Liss, Inc.
B‐type natriuretic peptide level in a patient with constrictive pericarditis
Authors: Brown Todd , Hollman Jay 
Published: November 2006

AbstractWe report the case of a 35‐year‐old man with constrictive pericarditis who had a B‐type natriuretic peptide (BNP) level of 129 pg/dl despite a left ventricular end diastolic pressure of 35 mmHg. We discuss a possible explanation for the relatively low BNP level given this patient's markedly elevated intracavitary pressures in the setting of constrictive pericarditis. © 2006 Wiley‐Liss, Inc.
Percutaneous coronary intervention with stent deployment in anomalously‐arising left circumflex coronary arteries
Authors: West Nick E.J. , McKenna Charles J. , Ormerod Oliver , Forfar J. Colin , Banning Adrian P. , Channon Keith M. 
Published: November 2006

AbstractBackground: Anomalous origin of the left circumflex coronary artery from the right sinus of Valsalva or proximal right coronary artery is the most common congenital coronary anatomical abnormality. Whether such vessels are particularly predisposed to atherosclerotic disease in their proximal portion remains controversial. Successful balloon angioplasty has been described, but thus far only six isolated cases of stent deployment in anomalous circumflex vessels have been described in the interventional literature. Methods: Single‐center retrospective case study of twenty‐two patients with anomalous circumflex coronary arteries. Twelve patients (11/12 male, average age (63 ± 3) years) underwent successful percutaneous coronary intervention (PCI) with stent deployment in the retroaortic segment of the anomalous vessel. Results: Significant obstructive coronary disease in the retroaortic portion was found in the majority of anomalous left circumflex vessels (16/22, 73%), but did not predict the presence of significant two or three vessel coronary disease (P = 0.14, 0.63). PCI was successful in all cases attempted, with favourable short/medium‐term event‐free survival. Conclusions: The retroaortic portion of anomalously‐arising circumflex coronary arteries is selectively predisposed to atherosclerotic disease. PCI to these vessels is feasible but may be technically challenging. © 2006 Wiley‐Liss, Inc.
Successful device closure of an acquired Gerbode defect
Authors: Trehan Vijay , Ramakrishnan S. , Goyal Naresh K. 
Published: November 2006

AbstractLeft ventricle to right atrial communications, collectively known as Gerbode defects, are usually congenital defects and surgical closure remains the treatment of choice. We report a rare case of Gerbode defect acquired following surgical closure of a ventricular septal defect. The defect was successfully closed percutaneously with an Amplatzer ventricular septal occluder. The patient remained symptom free with optimal result on echo at 6 months of follow‐up. This is the first reported case of successful device closure of an acquired Gerbode defect. © 2006 Wiley‐Liss, Inc.