bluuebunny/crossref_metadata_2025_split huggingface dataset:
Perceiving molecular evolution processes in Escherichia coliby comprehensive metabolite and gene expression profiling
Authors: Vijayendran Chandran , Barsch Aiko , Friehs Karl , Niehaus Karsten , Becker Anke , Flaschel Erwin 
Published: May 2008

Abstract
Background
Evolutionary changes that are due to different environmental conditions can be examined based on the various molecular aspects that constitute a cell, namely transcript, protein, or metabolite abundance. We analyzed changes in transcript and metabolite abundance in evolved and ancestor strains in three different evolutionary conditions - excess nutrient adaptation, prolonged stationary phase adaptation, and adaptation because of environmental shift - in two different strains of bacterium Escherichia coli K-12 (MG1655 and DH10B).

Results
Metabolite profiling of 84 identified metabolites revealed that most of the metabolites involved in the tricarboxylic acid cycle and nucleotide metabolism were altered in both of the excess nutrient evolved lines. Gene expression profiling using whole genome microarray with 4,288 open reading frames revealed over-representation of the transport functional category in all evolved lines. Excess nutrient adapted lines were found to exhibit greater degrees of positive correlation, indicating parallelism between ancestor and evolved lines, when compared with prolonged stationary phase adapted lines. Gene-metabolite correlation network analysis revealed over-representation of membrane-associated functional categories. Proteome analysis revealed the major role played by outer membrane proteins in adaptive evolution. GltB, LamB and YaeT proteins in excess nutrient lines, and FepA, CirA, OmpC and OmpA in prolonged stationary phase lines were found to be differentially over-expressed.

Conclusion
In summary, we report the vital involvement of energy metabolism and membrane-associated functional categories in all of the evolutionary conditions examined in this study within the context of transcript, outer membrane protein, and metabolite levels. These initial data obtained may help to enhance our understanding of the evolutionary process from a systems biology perspective.
CpG island density and its correlations with genomic features in mammalian genomes
Authors: Han Leng , Su Bing , Li Wen-Hsiung , Zhao Zhongming 
Published: May 2008

Abstract
Background
CpG islands, which are clusters of CpG dinucleotides in GC-rich regions, are considered gene markers and represent an important feature of mammalian genomes. Previous studies of CpG islands have largely been on specific loci or within one genome. To date, there seems to be no comparative analysis of CpG islands and their density at the DNA sequence level among mammalian genomes and of their correlations with other genome features.

Results
In this study, we performed a systematic analysis of CpG islands in ten mammalian genomes. We found that both the number of CpG islands and their density vary greatly among genomes, though many of these genomes encode similar numbers of genes. We observed significant correlations between CpG island density and genomic features such as number of chromosomes, chromosome size, and recombination rate. We also observed a trend of higher CpG island density in telomeric regions. Furthermore, we evaluated the performance of three computational algorithms for CpG island identifications. Finally, we compared our observations in mammals to other non-mammal vertebrates.

Conclusion
Our study revealed that CpG islands vary greatly among mammalian genomes. Some factors such as recombination rate and chromosome size might have influenced the evolution of CpG islands in the course of mammalian evolution. Our results suggest a scenario in which an increase in chromosome number increases the rate of recombination, which in turn elevates GC content to help prevent loss of CpG islands and maintain their density. These findings should be useful for studying mammalian genomes, the role of CpG islands in gene function, and molecular evolution.
Accuracy and Surgical Impact of Magnetic Resonance Imaging in Breast Cancer Staging: Systematic Review and Meta-Analysis in Detection of Multifocal and Multicentric Cancer
Authors: Houssami Nehmat , Ciatto Stefano , Macaskill Petra , Lord Sarah J. , Warren Ruth M. , Dixon J. Michael , Irwig Les 
Published: May 2008

Purpose We review the evidence on magnetic resonance imaging (MRI) in staging the affected breast to determine its accuracy and impact on treatment. Methods Systematic review and meta-analysis of the accuracy of MRI in detection of multifocal (MF) and/or multicentric (MC) cancer not identified on conventional imaging. We estimated summary receiver operating characteristic curves, positive predictive value (PPV), true-positive (TP) to false positive (FP) ratio, and examined their variability according to quality criteria. Pooled estimates of the proportion of women whose surgery was altered were calculated. Results Data from 19 studies showed MRI detects additional disease in 16% of women with breast cancer (N = 2,610). MRI incremental accuracy differed according to the reference standard (RS; P = .016) decreasing from 99% to 86% as the quality of the RS increased. Summary PPV was 66% (95% CI, 52% to 77%) and TP:FP ratio was 1.91 (95% CI, 1.09 to 3.34). Conversion from wide local excision (WLE) to mastectomy was 8.1% (95% CI, 5.9 to 11.3), from WLE to more extensive surgery was 11.3% in MF/MC disease (95% CI, 6.8 to 18.3). Due to MRI-detected lesions (in women who did not have additional malignancy on histology) conversion from WLE to mastectomy was 1.1% (95% CI, 0.3 to 3.6) and from WLE to more extensive surgery was 5.5% (95% CI, 3.1 to 9.5). Conclusion MRI staging causes more extensive breast surgery in an important proportion of women by identifying additional cancer, however there is a need to reduce FP MRI detection. Randomized trials are needed to determine the clinical value of detecting additional disease which changes surgical treatment in women with apparently localized breast cancer.
Prospective Study to Assess Short-Term Intra-Articular and Tenosynovial Changes in the Aromatase Inhibitor–Associated Arthralgia Syndrome
Authors: Morales Leilani , Pans Steven , Verschueren Kilian , Van Calster Ben , Paridaens Robert , Westhovens Rene , Timmerman Dirk , De Smet Luc , Vergote Ignace , Christiaens Marie-Rose , Neven Patrick 
Published: May 2008

PurposeArthralgia is an adverse class effect of aromatase inhibitors (AIs). To date, its exact mechanism remains unclear. The purpose of this study was to investigate the changes in clinical rheumatologic features and magnetic resonance imaging (MRI) of hands and wrists in AI and tamoxifen users.Patients and MethodsThis is a prospective single-center study including 17 consecutive postmenopausal patients with early breast cancer receiving either tamoxifen (n = 5) or an AI (n = 12). At baseline and after 6 months, patients filled in a rheumatologic history questionnaire and a rheumatologic examination including a grip strength test was done. At the same time points, MRI of both hands and wrists was performed. The primary end point was tenosynovial changes from baseline on MRI. Secondary end points were changes from baseline for morning stiffness, grip strength, and intra-articular fluid on MRI. Wilcoxon signed ranks was used to test changes from baseline and the Spearman correlation coefficient to assess the association between rheumatologic and MRI changes from baseline.ResultsAt 6 months, patients on AI had a decrease in grip strength (P = .0049) and an increase in tenosynovial changes (P = .0010). The decrease in grip strength correlated well with the tenosynovial changes on MRI (P = .0074). Only minor changes were seen in patients on tamoxifen. AI users reported worsening of morning stiffness and showed an increase in intra-articular fluid on MRI.ConclusionThe functional impairment of hands in the AI-associated arthralgia syndrome is characterized by tenosynovial changes on MRI correlating with a significant decrease in hand grip strength.
Phase I, Pharmacokinetic and Pharmacodynamic Study of the Anti–Insulinlike Growth Factor Type 1 Receptor Monoclonal Antibody CP-751,871 in Patients With Multiple Myeloma
Authors: Lacy Martha Q. , Alsina Melissa , Fonseca Rafael , Paccagnella M. Luisa , Melvin Carrie L. , Yin Donghua , Sharma Amarnath , Enriquez Sarano M. , Pollak Michael , Jagannath Sundar , Richardson Paul , Gualberto Antonio 
Published: May 2008

PurposeA phase I first-in-human study was conducted to characterize the safety, tolerability, pharmacokinetic, and pharmacodynamic properties of the anti–insulinlike growth factor 1 receptor (IGF-IR) monoclonal antibody CP-751,871.Patients and MethodsAfter informed consent and screening, 47 patients with multiple myeloma in relapse or refractory phase were enrolled into 11 dose-escalation cohorts of CP-751,871 at doses from 0.025 to 20 mg/kg for 4 weeks. Patients with less than a partial response to CP-751,871 treatment were eligible to receive CP-751,871 in combination with oral dexamethasone at the discretion of the investigator. Treatment with CP-751,871 and rapamycin with or without dexamethasone was also offered to patients enrolled in the 10 and 20 mg/kg cohorts with less than a partial response to initial therapy with single-agent CP-751,871.ResultsNo CP-751,871-related dose-limiting toxicities were identified. Plasma CP-751,871 concentrations increased with dose and concentration-time profiles were consistent with those of antibodies with target-mediated disposition. Importantly, CP-751,871 administration led to a decrease in granulocyte IGF-IR expression and serum insulinlike growth factor 1 accumulation at high doses, suggesting systemic IGF-IR inhibition. Tumor response was assessed according to the European Group for Blood and Marrow Transplantation criteria. Nine responses were reported in 27 patients treated with CP-751,871 in combination with dexamethasone. Of interest, two of the patients with a partial response were progressing from dexamethasone treatment at study entry.ConclusionThese data indicate that CP-751,871 is well tolerated and may constitute a novel agent in the treatment of multiple myeloma.
A New Model to Predict the Oxidation Kinetics of Zirconium Alloys in a Pressurized Water Reactor
Authors: Bouineau V. , Ambard A. , Bénier G. , Pêcheur D. , Godlewski J. , Fayette L. , Duverneix T. 
Published: May 2008

Abstract
The previous CEA corrosion code COCHISE provided satisfactory simulations of in-reactor corrosion of the fuel cladding when used in its validity range. In contrast, it could lead to hazardous predictions if applied out of this range due to the strongly linked parameters mainly based on the analysis of French pressurized water reactor (PWR) data. To predict the oxidation kinetics for new operating conditions or new materials, the CEA and EDF decided to develop a new model, named CORCY, which is based on a more phenomenological approach and uses separate parameters deduced from analytical experiments. The aim of this paper is to present the new model for Zircaloy-4 in PWR. The phenomenological approach is described. It is based on out- and in-pile data. Typically, since (1) the oxidation kinetics of zirconium alloys in autoclave are periodic, and (2) the oxide films formed in autoclave, in out-of-pile loop, and in-reactor all exhibit periodic lateral cracks with a period similar to the oxide thickness to transition, the oxidation kinetics in CORCY are characterized by a cyclic repetition of semi-parabolic law. Each model parameter is detailed. They are deduced separately from (a) oxidation tests performed in autoclave on fresh alloys to determine their kinetics; (b) oxidation tests performed in the out-of-pile corrosion loops Corail and Reggae to quantify the effects of thermo-hydraulic conditions; (c) data provided by Testing Material Reactors (OSIRIS and Halden reactor) during isothermal oxidation to determine the effects of irradiation; and (d) oxidation tests performed on pre-hydrided alloys to take into account the accelerated corrosion phase occurring, in reactor, for Zircaloy-4 at high burn-up. After describing both the phenomenological approach and the different model parameters, a comparison of measured and calculated corrosion data from French PWRs at a burn-up up to 65 GWd/tU is provided.
Feldeffekttransistoren für organische CMOS Technik (Field-Effect Transistors for Organic CMOS Technology)
Authors: Melzer Christian , von Seggern Heinz 
Published: May 2008

Zusammenfassung
Die Bereitstellung organischer CMOS Technik stellt eine Hürde für die Entwicklung organischer Logikbauelemente dar. Ausgehend von ambipolar wirkenden Feldeffekttransistoren werden in diesem Artikel Möglichkeiten zur Realisierung von organischen CMOS Bauteilen diskutiert. Konkret wird eine Methode vorgestellt, mit der n-sowie p-Typ Transistoren unter Beibehaltung des gleichen Bauteilaufbaus hergestellt werden können. Auf Basis dieser komplementär wirkenden OFETs lassen sich CMOS Inverter realisieren.
Smart Objects – Auswirkungen massengedruckter Einfachelektronik auf die IT-Infrastrukturen (Smart Objects – Effects of Mass-printed Electronics on IT Infrastructures)
Authors: Beigl Michael , Riedel Till , Decker Christian 
Published: May 2008

Zusammenfassung
Neue Entwicklungen in der Elektronik wie massengedruckte Einfachelektronik ermöglichen den Einsatz von Computersystemen an oder gar in Objekten, für die bisher ein solcher Einsatz nicht wirtschaftlich sinnvoll war. Dieser Beitrag untersucht die prinzipiellen Rahmenbedingungen bei der nahtlosen Integration von Smart Objects in bestehende IT-Strukturen. Probleme bei der Einbindung solcher Smart Objects in IT-Systeme — insbesondere hinsichtlich der Skalierbarkeit — werde thematisiert. Er zeigt zudem innovative Lösungsansätze wie “Active Interfaces” und Push der Geschäftslogik in Smart Objects. Der vorgestellte Systemansatz profitiert dabei von einer Vielzahl preiswerter, zusammenarbeitender Smart Objects und kann somit als Blaupause für die Informationsverarbeitung und Integration künftiger massengedruckter Elektroniksysteme in IT-Systeme gesehen werden.
Digitale Fabrik – Ein Vorgehensmodell für Virtual Reality in der Fabrik- und Anlagenplanung (Digital Factory – A Proceeding Model for Virtual Reality in Site and Plant Design)
Authors: Bracht Uwe , Eckert Clemens 
Published: May 2008

Zusammenfassung
Der vorliegende Artikel erläutert den Einsatz von Virtual Reality in der Fabrik- und Anlagenplanung, anhand einer am Institut für Maschinelle Anlagentechnik und Betriebsfestigkeit der TU Clausthal entwickelten Vorgehensweise. Dazu werden die bei Anwendung des beschriebenen Vorgehensmodells in Praxisprojekten feststellbaren Verlagerungen von Modellnutzungsintensität und Erstellungsaufwand beschrieben und interpretiert.
Effiziente Methoden zum Lösen von 3D-Puzzle-Problemen* (Efficient Methods for Solving 3D-Puzzle-Problems)
Authors: Winkelbach Simon 
Published: May 2008

Zusammenfassung
Das Zusammenfügen von 3D-Objekten aus Einzelteilen (3D-Puzzle-Problem) ist in vielen Bereichen von hoher Relevanz. Anwendungen finden sich beispielsweise in der Archäologie (Rekonstruktion von Artefakten), der Chirurgie (Richten von Knochenfrakturen), sowie der Bioinformatik (Protein-Docking) und Robotik (Fügen von Bauteilen). Dieser Artikel gibt einen Überblick über die Verfahren und erzielten Ergebnisse der Dissertation “Das 3D-Puzzle-Problem”, in der die gesamte Prozesskette von der Datenakquisition, über die allgemeine Registrierung von Oberflächen, bis hin zu speziellen Anwendungsfällen des 3D-Puzzle-Problems behandelt wird. Insbesondere werden neue Ansätze vorgestellt, mit denen Fragmente auf äußerst effiziente Weise und ohne Wissen über eine Initiallösung automatisch zusammengefügt werden können. Hierbei wird eine hohe Robustheit gegenüber Messungenauigkeiten, Fragmentschädigungen und Materialverschleiß erreicht. Darüber hinaus gelingt es, durch Ausnutzung von Symmetrieebenen und Achsen gebrochene Oberschenkel- und Beckenknochen virtuell zusammenzufügen und somit einen wichtigen Baustein für die computerassistierte Frakturbehandlung in der Chirurgie zu schaffen.
Outcome of Pregnancies at Risk for Neonatal Hemochromatosis Is Improved by Treatment With High-Dose Intravenous Immunoglobulin
Authors: Whitington Peter F. , Kelly Susan 
Published: May 2008

OBJECTIVES. Neonatal hemochromatosis is the result of severe fetal liver injury that seems to result from maternal-fetal alloimmunity. Women who have had an infant affected with neonatal hemochromatosis are at high risk in subsequent pregnancies for having another affected infant. This study was designed to determine whether therapy directed at limiting the severity of gestational alloimmunity can reduce the occurrence of severe neonatal hemochromatosis in infants of women at risk. A secondary objective was to use a prospectively collected data set to examine questions of vital interest about neonatal hemochromatosis.METHODS. Women with a history of pregnancy ending in documented neonatal hemochromatosis were treated with intravenous immunoglobulin at 1 g/kg of body weight weekly from week 18 until the end of gestation. Extensive data were prospectively collected regarding the gestational histories of the subjects. The outcomes of treated pregnancies were compared with those of previous affected pregnancies, which were used as historical controls.RESULTS. Forty-eight women were enrolled to be treated during 53 pregnancies. The gestational histories of these women demonstrated the high risk of occurrence of neonatal hemochromatosis: 92% of pregnancies at risk resulted in intrauterine fetal demise, neonatal death, or liver failure necessitating transplant. In contrast, with gestational therapy, the 53 at-risk gestations resulted in 3 failures and 52 infants who survived intact with medical therapy alone. When compared on a per-woman or per-infant basis, the outcome of gestation at risk for neonatal hemochromatosis was improved by gestational therapy.CONCLUSIONS. Neonatal hemochromatosis seems to be the result of a gestational alloimmune disease, and occurrence of severe neonatal hemochromatosis in at-risk pregnancies can be significantly reduced by treatment with high-dose intravenous immunoglobulin during gestation.
Occurrence and mass loadings of n-Alkanes in riverine runoff of the Pearl River Delta, South China: Global implications for levels and inputs
Authors: Wang Ji-Zhong , Ni Hong-Gang , Guan Yu-Feng , Zeng Eddy Y 
Published: May 2008

Abstract
Riverine runoff samples were collected monthly from March 2005 to February 2006 from the eight major outlets of the Pearl River Delta (PRD), South China, and analyzed to obtain the concentrations of n-alkanes in both the filtrate and particulate phases. The average concentrations of Σ(C15–C34) (i.e., sum of C15 to C34 normal alkanes) ranged from 0.06 to 2.97 μg/L (mean, 0.64 μg/L) in filtrate samples and from 1.00 to 98.8 μg/g (average, 19.8 μg/g dry weight) in particulate samples. Compared to results from around the world, the levels of hydrocarbon compounds in the PRD were at the high end of the global range. Evaluation of compositional indices of n-alkanes indicated that petroleum-related sources are the main contributor of n-alkanes found in the PRD, with minor contributions from high plant wax. Regression analyses appeared to suggest that n-alkanes are transported into the aquatic environment of the PRD via various pathways, and the transport mechanisms also are considerably influenced by the complex hydrologic conditions in the PRD. The annual riverine input of Σ(C15–C34) from the PRD to the coastal ocean was 360 tons/year, or the equivalent of approximately 8,800 tons/year of petroleum hydrocarbons. The emission of Σ(C15–C34) from all sources in the PRD was estimated at 39,000 tons/year, or 2.4 g/day per capita. Overall, the PRD contributes approximately 0.2% of the annual global input of n-alkanes to the coastal oceans, similar to the contributions of polycyclic aromatic hydrocarbons, further indicating that the PRD has been a significant source of hydrocarbon contamination to the global coastal marine environment.
Apparent tolerance of turkey vultures (Cathartes aura) to the non-steroidal anti-inflammatory drug diclofenac
Authors: Rattner Barnett A , Whitehead Maria A , Gasper Grace , Meteyer Carol U , Link William A , Taggart Mark A , Meharg Andrew A , Pattee Oliver H , Pain Deborah J 
Published: May 2008

Abstract
The nonsteroidal anti-inflammatory drug diclofenac is extremely toxic to Old World Gyps vultures (median lethal dose ∼0.1–0.2 mg/kg), evoking visceral gout, renal necrosis, and mortality within a few days of exposure. Unintentional secondary poisoning of vultures that fed upon carcasses of diclofenac-treated livestock decimated populations in the Indian subcontinent. Because of the widespread use of diclofenac and other cyclooxygenase-2 inhibiting drugs, a toxicological study was undertaken in turkey vultures (Cathartes aura) as an initial step in examining sensitivity of New World scavenging birds. Two trials were conducted entailing oral gavage of diclofenac at doses ranging from 0.08 to 25 mg/kg body weight. Birds were observed for 7 d, blood samples were collected for plasma chemistry (predose and 12, 24, and 48 h and 7 d postdose), and select individuals were necropsied. Diclofenac failed to evoke overt signs of toxicity, visceral gout, renal necrosis, or elevate plasma uric acid at concentrations greater than 100 times the estimated median lethal dose reported for Gyps vultures. For turkey vultures receiving 8 or 25 mg/kg, the plasma half-life of diclofenac was estimated to be 6 h, and it was apparently cleared after several days as no residues were detectable in liver or kidney at necropsy. Differential sensitivity among avian species is a hallmark of cyclooxygenase-2 inhibitors, and despite the tolerance of turkey vultures to diclofenac, additional studies in related scavenging species seem warranted.
Auditor Independence: A Focus on the SEC Independence Rules
Authors: Gramling Audrey A. , Karapanos Vassilios 
Published: May 2008

Auditor independence is an important underpinning of the federal securities laws. These laws require that registrants' financial statements filed with the Securities and Exchange Commission (SEC) be audited by independent public accountants. The focus on independence for public company auditors was increased in light of the requirements of the Sarbanes-Oxley Act of 2002 to strengthen auditor independence.
These instructional resources provide background information on the current SEC auditor independence rules. After becoming familiar with these rules, you will have the opportunity to complete several case scenarios that address: (1) hypothetical settings that may represent violations of the SEC independence rules, (2) possible actions that an audit committee might take when it determines that the SEC independence rules may have been violated, and (3) possible alternatives to the current SEC independence rules that could achieve the desired public policy goals of objective audits and investor confidence.