bluuebunny/crossref_metadata_2025_split huggingface dataset:
DNA Hypomethylation Causes Bile Duct Defects in Zebrafish and Is a Distinguishing Feature of Infantile Biliary Atresia §Δ
Authors: Matthews Randolph P. , EauClaire Steven F. , Mugnier Monica , Lorent Kristin , Cui Shuang , Ross Megan M. , Zhang Zhe , Russo Pierre , Pack Michael 
Published: December 2010

Abstract

Infantile cholestatic disorders arise in the context of progressively developing intrahepatic bile ducts. Biliary atresia (BA), a progressive fibroinflammatory disorder of extra- and intrahepatic bile ducts, is the most common identifiable cause of infantile cholestasis and the leading indication for liver transplantation in children. The etiology of BA is unclear, and although there is some evidence for viral, toxic, and complex genetic causes, the exclusive occurrence of BA during a period of biliary growth and remodeling suggests an importance of developmental factors. Interestingly, interferon-γ (IFN-γ) signaling is activated in patients and in the frequently utilized rhesus rotavirus mouse model of BA, and is thought to play a key mechanistic role. Here we demonstrate intrahepatic biliary defects and up-regulated hepatic expression of IFN-γ pathway genes caused by genetic or pharmacological inhibition of DNA methylation in zebrafish larvae. Biliary defects elicited by inhibition of DNA methylation were reversed by treatment with glucocorticoid, suggesting that the activation of inflammatory pathways was critical. DNA methylation was significantly reduced in bile duct cells from BA patients compared to patients with other infantile cholestatic disorders, thereby establishing a possible etiologic link between decreased DNA methylation, activation of IFN-γ signaling, and biliary defects in patients.

Conclusion:

Inhibition of DNA methylation leads to biliary defects and activation of IFN-γ-responsive genes, thus sharing features with BA, which we determine to be associated with DNA hypomethylation. We propose epigenetic activation of IFN-γ signaling as a common etiologic mechanism of intrahepatic bile duct defects in BA. (Hepatology 2011;)
A smoking‐based carcinogenesis model for lung cancer risk prediction
Authors: Foy Millennia , Spitz Margaret R. , Kimmel Marek , Gorlova Olga Y. 
Published: December 2010

AbstractLung cancer is the leading cancer killer for both men and women worldwide. Over 80% of lung cancers are attributed to smoking. In this analysis, the authors propose to use a two‐stage clonal expansion (TSCE) model to predict an individual's lung cancer risk based on gender and smoking history. The TSCE model is traditionally fitted to prospective cohort data. Here, the authors describe a new method that allows for the reconstruction of cohort data from the combination of risk factor data obtained from a case‐control study, and tabled incidence/mortality rate data, and discuss alternative approaches. The method is applied to fit a TSCE model based on smoking. The fitted model is validated against independent data from the control arm of a lung cancer chemoprevention trial, CARET, where it accurately predicted the number of lung cancer deaths observed.
Frequency of mismatch repair deficiency in ovarian cancer: a systematic review This article is a US Government work and, as such, is in the public domain of the United States of America.
Authors: Murphy Megan A. , Wentzensen Nicolas 
Published: December 2010

AbstractLoss of mismatch repair (MMR) capacity may represent an important tumor initiating mechanism in ovarian cancer. We conducted a systematic review to analyze the frequency of microsatellite instability (MSI), immunohistochemical (IHC) staining for MMR proteins, and hypermethylation of the MLH1 promoter region in ovarian cancers. Studies examining MSI, loss of MMR gene expression by IHC staining and MLH1 promoter hypermethylation in ovarian cancer were identified by a systematic literature search of the PubMed electronic database through August 31, 2009. Pertinent data was extracted from eligible studies and estimates for pooled proportions were computed using random effects models. The pooled proportion of MSI detection was 0.10 (95% CI, 0.06−0.14) among 1,234 cases in 22 studies. Dinonucleotide markers had a higher frequency of instability than mononucleotide markers. The pooled proportion of MLH1 or MSH2 staining loss was 0.06 (95% CI, 0.01−0.17) among 474 cases in three studies, with a higher frequency of loss in MLH1. The pooled proportion of MLH1 methylation was 0.10 (95% CI, 0.06−0.15) among 672 cases in seven studies. Data reporting MSI and loss of MMR staining in the same cases was limited. Although MMR deficiency was found in all histologic subtypes, endometrioid cancers had the highest proportion. Approximately 10% of unselected ovarian cancers are related to MMR deficiency. While MMR deficiency is associated with improved survival in other MMR‐deficiency related cancer sites, epidemiological and clinical factors related to the MMR‐deficient phenotype have not been adequately studied in ovarian cancer to date.
Palladium‐Catalyzed Arylation Reactions: A Mechanistic Perspective
Authors: Livendahl Madeleine , Echavarren Antonio M. 
Published: December 2010

AbstractAfter being restricted for the intramolecular formation of C–C bonds, the palladium catalyzed arylation reaction has been extended for the intermolecular synthesis of biaryls systems. Many of these reactions have been demonstrated to proceed by mechanisms that involve a concerted metalation–deprotonation, in which the base plays an important role in the proton abstraction. Other mechanisms based on electrophilic aromatic substitution and on PdII/PdIVor PdII/PdIIIcatalytic cycles have also been proposed. This review summarizes the most important recent advancements on the mechanistic understanding of the different types of palladium‐catalyzed arylations reactions.
Laminopathies and lamin‐associated signaling pathways
Authors: Maraldi Nadir M. , Capanni Cristina , Cenni Vittoria , Fini Milena , Lattanzi Giovanna 
Published: December 2010

AbstractLaminopathies are genetic diseases due to mutations or altered post‐translational processing of nuclear envelope/lamina proteins. The majority of laminopathies are caused by mutations in the LMNA gene, encoding lamin A/C, but manifest as diverse pathologies including muscular dystrophy, lipodystrophy, neuropathy, and progeroid syndromes. Lamin‐binding proteins implicated in laminopathies include lamin B2, nuclear envelope proteins such as emerin, MAN1, LBR, and nesprins, the nuclear matrix protein matrin 3, the lamina‐associated polypeptide, LAP2alpha and the transcriptional regulator FHL1. Thus, the altered functionality of a nuclear proteins network appears to be involved in the onset of laminopathic diseases. The functional interplay among different proteins involved in this network implies signaling partners. The signaling effectors may either modify nuclear envelope proteins and their binding properties, or use nuclear envelope/lamina proteins as platforms to regulate signal transduction. In this review, both aspects of lamin‐linked signaling are presented and the major pathways so far implicated in laminopathies are summarized. J. Cell. Biochem. 112: 979–992, 2011. © 2010 Wiley‐Liss, Inc.
Essential roles of sphingosine 1‐phosphate receptor types 1 and 3 in human hepatic stellate cells motility and activation
Authors: Liu Xihong , Yue Shi , Li Changyong , Yang Lin , You Hong , Li Liying 
Published: December 2010

AbstractThe biological roles of sphingosine 1‐phosphate (S1P) and S1P receptors (S1PRs) have been broadly investigated. However, at present pathophysiological roles of S1P/S1PRs axis in liver fibrosis are not well defined. Here, we investigated the functions of S1P/S1PRs axis in human hepatic stellate cells (HSC) line, LX‐2 cells. We found that S1PR types 1, 2 and 3 (S1PR1–3) are clearly detected in LX‐2 cells, as determined by RT‐PCR, Western blot and immunocytochemistry analysis. S1P exerted a powerful migratory action on LX‐2 cells, as determined in Boyden chambers, and stimulated fibrogenic activity of LX‐2 cells, as demonstrated by increase of expression of smooth muscle α‐actin, procollagen α1(I) and α1(III) and total hydroxyproline content. Moreover, the effects of S1P were mimicked by S1PR1 agonist SEW2871, and abrogated by W146 (S1PR1 antagonist) and/or silencing S1PR1, three expression with small interfering RNA, suggesting the main roles of S1PR1 and 3. However, studies with S1PR2 antagonist JTE‐013 and silencing S1PR2 expression indicated that S1PR2 negatively regulated S1P‐induced cell migration. Interestingly, exogenously added S1P induced significant up‐regulation of sphingosine kinase‐1 and the synthesis of additional S1P, and expression of S1PR1,3, but not S1PR2. In conclusion, our data have identified an additional function regulated by S1P/S1PR1,3 axis involving migration and fibrogenic activation of HSCs. These results suggest that selective modulation of S1PR activity may represent a new antifibrotic strategy. J. Cell. Physiol. 226: 2370–2377, 2011. © 2010 Wiley‐Liss, Inc.
Sonication cultures of explanted components as an add‐on test to routinely conducted microbiological diagnostics improve pathogen detection
Authors: Holinka Johannes , Bauer Leonhard , Hirschl Alexander M. , Graninger Wolfgang , Windhager Reinhard , Presterl Elisabeth 
Published: December 2010

AbstractThe purpose of this study was to improve the pathogen detection in prosthetic joint infections, particularly to evaluate the feasibility of the sonication culture method in the clinical routine. Explanted components of all patients with presumptive prosthetic or implant infection were sonicated separately in sterile containers to dislodge the adherent bacteria from the surfaces and cultured. The results of sonication culture were compared to the conventional tissue culture. We investigated 60 consecutive patients with loosening of the prostheses or implants Forty patients had septic and 20 aseptic loosening (24 knee prostheses, 21 hip prostheses, 6 mega‐prostheses, 2 shoulder prostheses, 6 osteosynthesis, 1 spinal instrumentation). The sensitivity of sonication fluid culture was 83.3%, of single positive tissue culture was 72.2% and 61.1% when two or more cultures yielded the same microorganism. In patients receiving antibiotic therapy the sensitivity was 65.9%, 57.5%, and 42.5%, respectively. Pathogens detected in a single tissue culture as well as in sonication culture yielded a significantly higher rate of prosthetic infection than conventional tissue culture alone (p = 0.008), even in patients receiving continuous antibiotic therapy before explantation (p = 0.016). The sonication method represents an essential add‐on in pathogen detection compared to conventional tissue culture. © 2010 Orthopaedic Research Society. Published by Wiley Periodicals, Inc. J Orthop Res 29:617–622, 2011
Effects of lime and sewage sludge on soil, pasture production, and tree growth in a six‐year‐old Populus canadensis Moench silvopastoral system
Authors: Mosquera‐Losada M. Rosa , Morán‐Zuloaga Daniel , Rigueiro‐Rodriguez Antonio 
Published: December 2010

AbstractIn many regions worldwide, silvopastoral systems are implemented to enable sustainable land use allowing short, medium, and long‐term economic returns. However, the short‐term production in silvopastoral systems is often limited due to nonappropriate soil‐fertility management. This study evaluated the effects of two doses of lime (0 and 2.5 t CaCO3 ha–1) and three sewage‐sludge treatments (0, 200, and 400 kg total N ha–1 y–1 applied in 2 consecutive years) on soil characteristics (soil pH, soil organic matter [SOM], soil nitrogen, cation‐exchange capacity [CEC]), pasture production, and tree growth in a silvopastoral system of Populus × canadensis Moench in Galicia, northern Spain during 6 years after establishment. Soil pH increased during the experimental period for all treatments, although this effect was more pronounced after lime application. Changes in SOM and soil nitrogen content were not consistent over time, but sewage‐sludge application seemed to result in higher values. Higher CEC was found for treatments with lime and sewage‐sludge application. Following incorporation of lime and sewage sludge, pasture production was significantly enhanced (cumulative pasture production 51.9 t DM ha–1 for Lime/N400 compared to 39.0 t DM ha–1 for No lime/N0). This higher pasture production also affected tree growth due to more severe competition between pasture and tree resulting in slower tree growth. Liming and application of sewage sludge are relevant measures to improve soil fertility and thereby optimizing the overall production of silvopastoral systems. However, it is important not to overintensify pasture production to ensure adequate tree growth.
Measuring the CO2 production from maize‐straw‐amended soil columns— a comparison of four methods
Authors: Rottmann Nils , Georg Joergensen Rainer 
Published: December 2010

AbstractA soil‐column experiment with maize‐straw application at different depths was carried out to investigate the accuracy of CO2‐measurement systems in a greenhouse experiment with sandy and loamy soils. The classical approach of CO2 absorption in NaOH solution was compared with three other methods using dynamic chambers. These methods were gas chromatography (GC), a portable infrared analyzer (IR), and a portable photo‐acoustic system (PAS). The cumulative CO2 production over the 57‐day incubation period was significantly affected by the method and soil‐specifically by the treatments. The NaOH and GC method always formed a pair of lowest cumulative CO2 production in all treatments with maize‐straw addition. In the treatments with bottom application of the maize straw, IR and PAS methods gave values at identical levels in both soils. In the treatments with top application of the maize straw, the IR method gave significantly highest values in the sandy soil and the PAS method in the loamy soil. The correlation coefficients between the cumulative CO2 production of the three dynamic‐chamber methods (GC, IR, and PAS) and the static NaOH method were all significant, with r values between 0.90 and 0.93. The C balance can be used for testing the plausibility of CO2‐production data. Roughly 102% (NaOH and GC) and 114% (IR and PAS) were recovered, including the CO2‐production data in the C balance of the sandy soil. The respective data were 97% (NaOH and GC) and 104% (IR and PAS) for the loamy soil.
Application of the DNDC model to predict N2O emissions from sandy arable soils with differing fertilization in a long‐term experiment
Authors: Ludwig Bernard , Jäger Nadine , Priesack Eckart , Flessa Heinz 
Published: December 2010

AbstractModeling crop growth and soil N dynamics is difficult due to the complex nature of soil–plant systems. In several studies, the DNDC model has been claimed to be well‐suited for this purpose whereas in other studies applications of the model were less successful. Objectives of this study were to test a calibration and validation scheme for DNDC‐model applications to describe a field experiment with spring wheat on a sandy soil near Darmstadt (SW Germany) using different fertilizer types (either application of mineral fertilizer and straw—MSI; or application of farmyard manure—FYM) and rates (low—MSIL, FYML; and medium—MSIM, FYMM). The model test is based on a model parameterization to best describe the case MSIL and applies this parameterization for a retrospective simulation of the other cases (MSIM, FYML, FYMM) including crop growth and N2O emissions. Soil water contents were not accurately simulated using either the DNDC default values for a loamy sand or for the next finer texture class or using results from the pedotransfer function provided by ROSETTA. After successful calibration of the soil water flow model using a soil texture class that led to the best fit of the measured water content data, grain yield of spring wheat and cumulative N2O emission were slightly underestimated by DNDC and were between 91% and 86% of the measured data. A subsequent calibration of the yields and cumulative N2O emissions from soils of the MSIL treatment gave a good prediction of crop growth and N2O emissions in the MSIM treatment, but a marked underestimation of yields of the FYM treatments. Cumulative N2O emissions were predicted well for all MSI and FYM treatments, but seasonal dynamics were not. Overall, our results indicated that for the sandy soil in Germany, site‐specific calibration was essentially required for the soil hydrology and that a calibration was useful for a subsequent prediction where greater amounts of the same fertilizer were used, but not useful for a prediction with a different fertilizer type.
Raman spectroscopy of gallium‐ and zinc‐based hydrotalcites
Authors: Palmer Sara J. , Frost Ray L. , Grand Laure‐Marie 
Published: December 2010

AbstractInsight into the unique structure of hydrotalcites (HTs) has been obtained using Raman spectroscopy. Gallium‐containing HTs of formula Zn4 Ga2(CO3)(OH)12 · xH2O (2:1 ZnGa‐HT), Zn6 Ga2(CO3)(OH)16 · xH2O (3:1 ZnGa‐HT) and Zn8 Ga2(CO3)(OH)18 · xH2O (4:1 ZnGa‐HT) have been successfully synthesised and characterised by X‐ray diffraction (XRD) and Raman spectroscopy. The d(003) spacing varies from 7.62 Å for the 2:1 ZnGa‐HT to 7.64 Å for the 3:1 ZnGa‐HT. The 4:1 ZnGa‐HT showed a decrease in the d(003) spacing, compared to the 2:1 and 3:1 compounds. Raman spectroscopy complemented with selected infrared data has been used to characterise the synthesised gallium‐containing HTs. Raman bands observed at around 1050, 1060 and 1067 cm−1 are attributed to the symmetric stretching modes of the (CO32−) units. Multiple ν3 (CO32−) antisymmetric stretching modes are found between 1350 and 1520 cm−1, confirming multiple carbonate species in the HT structure. The splitting of this mode indicates that the carbonate anion is in a perturbed state. Raman bands observed at 710 and 717 cm−1 and assigned to the ν4 (CO32−) modes support the concept of multiple carbonate species in the interlayer. Copyright © 2010 John Wiley & Sons, Ltd.
The growth of the passive film on iron in 0.05 M NaOH studied in situ by Raman microspectroscopy and electrochemical polarization. Part II: In situ Raman spectra of the passive film surface during growth by electrochemical polarization
Authors: Nieuwoudt M. K. , Comins J. D. , Cukrowski I. 
Published: December 2010

AbstractThe composition of the passive film formed on iron in 0.05 M NaOH was analyzed in situ with Raman microspectroscopy with preresonance enhancement during its growth by cyclic potentiodynamic polarization. The surface comprised more than one iron oxide and oxyhydroxide compound whose composition changed during the anodic and cathodic sweeps within successive cycles leading to film growth. The relative amounts of the different iron compounds in the film at selected potentials were determined from the spectra using multivariate curve resolution (MCR) with alternating least squares analysis. Individual spectra of six different such compounds, comprising Fe3O4 (magnetite), γ‐Fe2O3 (maghemite), α‐Fe2O3 (hematite), α‐FeOOH (goethite), δ‐FeOOH (feroxyhyte) and γ‐FeOOH (lepidocrocite), were used as pure component spectra for the MCR optimization. The results obtained over the first 15 cycles indicate that α‐FeOOH, γ‐FeOOH, δ‐FeOOH and γ‐Fe2O3 were present in the film at the beginning of the passive region of the anodic polarization. The amount of water in the film was also observed to increase at this potential range. Further into the passive region (at more positive potentials), a decrease in the amount of water, which was accompanied by a decrease in α‐FeOOH and γ‐FeOOH in favor of an increase in the amount of γ‐Fe2O3, was observed. Fe3O4 and α‐Fe2O3 were not detected on the surface. With increasing number of cycles, the surface became increasingly amorphous or hydrated. Copyright © 2010 John Wiley & Sons, Ltd.
Raman characterization of localized CdS nanostructures synthesized by UV irradiation in sol–gel silica matrices
Authors: Raulin Katarzyna , Turrell Sylvia , Capoen Bruno , Kinowski Christophe , Thanh Tran Van Thi , Bouazaoui Mohamed , Cristini Odile 
Published: December 2010

AbstractA new technique of UV irradiation has been used for the first time to create microstructures of CdS nanoparticles in bulk xerogels. Porous silica matrices, which were first soaked in a solution containing CdS precursors, were subjected to irradiation using a nanopulsed ArF laser with a wavelength of 193 nm and a repetition rate of 10 Hz.Resonant micro‐Raman spectra, recorded using the 325‐nm line of a He‐Cd laser (with a continuous power less than 0.5 mW so as to avoid the thermal formation of nanoparticles) made it possible to identify CdS nanoparticles within the inscribed yellow zones and also to estimate the average particle size (3.6 to 8.0 nm, depending on the number of UV pulses used). The emission of CdS particles embedded in the silica matrix under excitation at 351.1 nm was studied by photoluminescence spectroscopy. It was then possible to show the effect of the number of pulses on the electronic structure of the nanocrystals.Finally, Raman spectra were used to monitor the structural changes in the silica matrix caused by the irradiation. It was found that the pulsed UVirradiation resulted in a local densification of the matrix, which was compensated for by a depolymerization process of the SiOSi network. In spite of this pulsed irradiation and the resulting structural depolymerization, no apparent ablation or cracking of the samples was observed. Copyright © 2010 John Wiley & Sons, Ltd.
Religious tourism and its management: the hajj in Saudi Arabia
Authors: Henderson Joan Catherine 
Published: December 2010

AbstractReligion and tourism share a close relationship in which the former motivates travel and is a source of assorted visitor attractions. Pilgrimage is one expression of the ties between the two and the paper identifies key pilgrimage tourism issues pertaining to demand and provision that are discussed within the context of the contemporary hajj. The hajj by Muslims to the cities they deem holy in Saudi Arabia is a distinctive illustration that involves the mass movement of pilgrims every year. Numbers are strictly controlled, but set to rise as the government pursues a policy of expanding space at certain holy sites and encouraging an increase in the supply of accommodation and other amenities as well as enhancing supporting infrastructure. Some projects are very ambitious, leading to questions about whether the pace of development is sustainable. The purpose of the study is to improve understanding of the uniqueness and significance of the hajj phenomenon and illuminate the challenges of managing large‐scale religious tourism events in the changing world of the twenty‐first century. Copyright © 2010 John Wiley & Sons, Ltd.