bluuebunny/crossref_metadata_2025_split huggingface dataset:
Mechanisms for an effect of acetylcysteine on renal function after exposure to radio-graphic contrast material: study protocol
Authors: Sandilands Euan A , Cameron Sharon , Paterson Frances , Donaldson Sam , Briody Lesley , Crowe Jane , Donnelly Julie , Thompson Adrian , Johnston Neil R , Mackenzie Ivor , Uren Neal , Goddard Jane , Webb David J , Megson Ian L , Bateman Nicholas , Eddleston Michael 
Published: February 2012

Abstract

Background
Contrast-induced nephropathy is a common complication of contrast administration in patients with chronic kidney disease and diabetes. Its pathophysiology is not well understood; similarly the role of intravenous or oral acetylcysteine is unclear. Randomized controlled trials to date have been conducted without detailed knowledge of the effect of acetylcysteine on renal function. We are conducting a detailed mechanistic study of acetylcysteine on normal and impaired kidneys, both with and without contrast. This information would guide the choice of dose, route, and appropriate outcome measure for future clinical trials in patients with chronic kidney disease.

Methods/Design
We designed a 4-part study. We have set up randomised controlled cross-over studies to assess the effect of intravenous (50 mg/kg/hr for 2 hrs before contrast exposure, then 20 mg/kg/hr for 5 hrs) or oral acetylcysteine (1200 mg twice daily for 2 days, starting the day before contrast exposure) on renal function in normal and diseased kidneys, and normal kidneys exposed to contrast. We have also set up a parallel-group randomized controlled trial to assess the effect of intravenous or oral acetylcysteine on patients with chronic kidney disease stage III undergoing elective coronary angiography. The primary outcome is change in renal blood flow; secondary outcomes include change in glomerular filtration rate, tubular function, urinary proteins, and oxidative balance.

Discussion
Contrast-induced nephropathy represents a significant source of hospital morbidity and mortality. Over the last ten years, acetylcysteine has been administered prior to contrast to reduce the risk of contrast-induced nephropathy. Randomized controlled trials, however, have not reliably demonstrated renoprotection; a recent large randomized controlled trial assessing a dose of oral acetylcysteine selected without mechanistic insight did not reduce the incidence of contrast-induced nephropathy. Our study should reveal the mechanism of effect of acetylcysteine on renal function and identify an appropriate route for future dose response studies and in time randomized controlled trials.

Trial registration
Clinical Trials.gov: NCT00558142; EudraCT: 2006-003509-18.
Deciphering the role of Paenibacillus strain Q8 in the organic matter recycling in the acid mine drainage of Carnoulès
Authors: Delavat François , Phalip Vincent , Forster Anne , Lett Marie-Claire , Lièvremont Didier 
Published: February 2012

AbstractBackgroundThe recycling of the organic matter is a crucial function in any environment, especially in oligotrophic environments such as Acid Mine Drainages (AMDs). Polymer-degrading bacteria might play an important role in such ecosystem, at least by releasing by-products useful for the rest of the community. In this study, physiological, molecular and biochemical experiments were performed to decipher the role of aPaenibacillusstrain isolated from the sediment of Carnoulès AMD.ResultsEven thoughPaenibacillussp. strain Q8 was isolated from an oligotrophic AMD showing an acidic pH, it developed under both acidic and alkaline conditions and showed a heterotrophic metabolism based on the utilization of a broad range of organic compounds. It resisted to numerous metallic stresses, particularly high arsenite (As(III)) concentrations (> 1,800 mg/L). Q8 was also able to efficiently degrade polymers such as cellulose, xylan and starch. Function-based screening of a Q8 DNA-library allowed the detection of 15 clones with starch-degrading activity and 3 clones with xylan-degrading activity. One clone positive for starch degradation carried a single gene encoding a "protein of unknown function". Amylolytic and xylanolytic activities were measured both in growing cells and with acellular extracts of Q8. The results showed the ability of Q8 to degrade both polymers under a broad pH range and high As(III) and As(V) concentrations. Activity measurements allowed to point out the constitutive expression of the amylase genes and the mainly inducible expression of the xylanase genes. PACE demonstrated the endo-acting activity of the amylases and the exo-acting activity of the xylanases.ConclusionsAMDs have been studied for years especially with regard to interactions between bacteria and the inorganic compartment hosting them. To date, no study reported the role of microorganisms in the recycling of the organic matter. The present work suggests that the strain Q8 might play an important role in the community by recycling the scarce organic matter (cellulose, hemicellulose, starch...), especially when the conditions change. Furthermore, function-based screening of a Q8 DNA library allowed to assign an amylolytic function to a gene previously unknown. AMDs could be considered as a reservoir of genes with potential biotechnological properties.
Protein tyrosine phosphatase receptor delta acts as a neuroblastoma tumor suppressor by destabilizing the aurora kinase a oncogene
Authors: Meehan Maria , Parthasarathi Laavanya , Moran Niamh , Jefferies Caroline A , Foley Niamh , Lazzari Elisa , Murphy Derek , Ryan Jacqueline , Ortiz Berenice , Fabius Armida W M , Chan Timothy A , Stallings Raymond L 
Published: February 2012

AbstractBackgroundProtein tyrosine phosphatase receptor delta (PTPRD) is a member of a large family of protein tyrosine phosphatases which negatively regulate tyrosine phosphorylation. Neuroblastoma is a major childhood cancer arising from precursor cells of the sympathetic nervous system which is known to acquire deletions and alterations in the expression patterns ofPTPRD, indicating a potential tumor suppressor function for this gene. The molecular mechanism, however, by which PTPRD renders a tumor suppressor effect in neuroblastoma is unknown.ResultsAs a molecular mechanism, we demonstrate that PTPRD interacts with aurora kinase A (AURKA), an oncogenic protein that is over-expressed in multiple forms of cancer, including neuroblastoma. Ectopic up-regulation of PTPRD in neuroblastoma dephosphorylates tyrosine residues in AURKA resulting in a destabilization of this protein culminating in interfering with one of AURKA's primary functions in neuroblastoma, the stabilization of MYCN protein, the gene of which is amplified in approximately 25 to 30% of high risk neuroblastoma.ConclusionsPTPRD has a tumor suppressor function in neuroblastoma through AURKA dephosphorylation and destabilization and a downstream destabilization of MYCN protein, representing a novel mechanism for the function of PTPRD in neuroblastoma.
Clinicopathologic study of E-cadherin/beta-catenin complex, and topoisomerase-II in a series of 71 liposarcoma cases
Authors: Gogou Pinelopi , Pakos Emilios , Batistatou Anna , Panelos Ioannis , Briasoulis Evangelos , Stefanou Dimitrios , Apostolikas Nikoforos , Tsekeris Periclis 
Published: February 2012

Abstract

Background
To investigate the expression of E-cadherin, beta-catenin and topoisomerase-II alpha and examine their clinical relevance in liposarcomas.

Materials and methods
The expression of E-cadherin, beta-catenin and topoisomerase II alpha was examined immunohistochemically on formalin-fixed paraffin-embedded tissue specimens from 71 patients who underwent surgical treatment for liposarcomas of the extremities or the retroperitoneum in two major cancer reference centres between 1990 and 2000. Detailed medical notes were available for all patients who were followed for median 82 months (range 5 to 215 months). Obtained expression data were weighted against clinical and pathology parameters of clinical relevance.

Results
Patients were mostly male (59%), median age was 56 years for the liposarcomas of the extremities and 60 years for the retroperitoneal liposarcomas. The tumours were of diverse histology, grade and size (median diameters 7 and 17 cm for tumours of the extremities and retroperitoneum respectively). Expression of β-catenin protein was weakly detected in 15 cases (21.1%). Similarly weak expression of topoisomerase II-alpha was detected in 14 (19.7%) cases of which only two had more than 20% of tumor cells stained positive. E-cadherin was not detected in the studied cohort of liposarcomas. We did not detect associations between the expression of the above proteins by liposarcoma cells and clinical outcome.

Conclusions
Liposarcomas do not express E-cadherin, which matches the absence of epithelioid differentiation in this sarcoma subtype, and have low topoisomerase II-alpha expression, which justifies to some extend their resistance to anthracycline-based chemotherapy.
PhosphoRice: a meta-predictor of rice-specific phosphorylation sites
Authors: Que Shufu , Li Kuan , Chen Min , Wang Yongfei , Yang Qiaobin , Zhang Wenfeng , Zhang Baoqian , Xiong Bangshu , He Huaqin 
Published: February 2012

Abstract

Background
As a result of the growing body of protein phosphorylation sites data, the number of phosphoprotein databases is constantly increasing, and dozens of tools are available for predicting protein phosphorylation sites to achieve fast automatic results. However, none of the existing tools has been developed to predict protein phosphorylation sites in rice.

Results
In this paper, the phosphorylation site predictors, NetPhos 2.0, NetPhosK, Kinasephos, Scansite, Disphos and Predphosphos, were integrated to construct meta-predictors of rice-specific phosphorylation sites using several methods, including unweighted voting, unreduced weighted voting, reduced unweighted voting and weighted voting strategies. PhosphoRice, the meta-predictor produced by using weighted voting strategy with parameters selected by restricted grid search and conditional random search, performed the best at predicting phosphorylation sites in rice. Its Matthew's Correlation Coefficient (MCC) and Accuracy (ACC) reached to 0.474 and 73.8%, respectively. Compared to the best individual element predictor (Disphos_default), PhosphoRice archieved a significant increase in MCC of 0.071 (P < 0.01), and an increase in ACC of 4.6%.

Conclusions
PhosphoRice is a powerful tool for predicting unidentified phosphorylation sites in rice. Compared to the existing methods, we found that our tool showed greater robustness in ACC and MCC. PhosphoRice is available to the public at http://bioinformatics.fafu.edu.cn/PhosphoRice.
Differences and discrepancies between 2005 and 2008 Abbreviated Injury Scale versions - time to standardise
Authors: Ringdal Kjetil G , Hestnes Morten , Palmer Cameron S 
Published: February 2012

Abstract
The aim of this letter is to facilitate the standardisation of Abbreviated Injury Scale (AIS) codesets used to code injuries in trauma registries. We have compiled a definitive list of the changes which have been implemented between the AIS 2005 and Update 2008 versions. While the AIS 2008 codeset appears to have remained consistent since its release, we have identified discrepancies between the codesets in copies of AIS 2005 dictionaries. As a result, we recommend that use of the AIS 2005 should be discontinued in favour of the Update 2008 version.
Waveform tomography of field vibroseis data using an approximate 2D geometry leads to improved velocity models
Authors: Smithyman Brendan R. , Clowes Ronald M. 
Published: February 2012

Waveform tomography, a combination of traveltime tomography (or inversion) and waveform inversion, is applied to vibroseis first-arrival data to generate an interpretable model of P-wave velocity for a site in the Nechako Basin, south-central British Columbia, Canada. We use constrained 3D traveltime inversion followed by 2D full-waveform inversion to process long-offset (14.4 km) first-arrival refraction waveforms, resulting in a velocity model of significantly higher detail than a conventional refraction-statics model generated for a processing workflow. The crooked-line acquisition of the data set makes 2D full-waveform inversion difficult. Thus, a procedure that improves the tractability of waveform tomography processing of vibroseis data recorded on crooked roads is developed to generate a near-surface ([Formula: see text]) velocity model for the study area. The data waveforms are first static corrected using a time shift determined by 3D raytracing, which accounts for the crossline offsets produced by the crooked-line acquisition. The velocity model generated from waveform tomography exhibits substantial improvement when compared with a conventional refraction-statics model. It also shows improved resolution of sharp discontinuities and low-velocity regions when compared to the model from traveltime tomography alone, especially in regions where the geometry errors are moderate. Interpretation of the near-surface velocity model indicates possible subbasins in the Nechako Basin and delineates the Eocene volcanic rocks of the study area. This approach limits the ability of the full-waveform inversion to fit some propagation modes; however, the tractability of the inversion in the near-surface region is improved. This new development is especially useful in studies that do not warrant 3D seismic acquisition and processing.
Continual and partial MEK inhibition ameliorates cardio-facio-cutaneous phenotypes in zebrafish
Authors: Anastasaki Corina , Rauen Katherine A. , Patton E. Elizabeth 
Published: February 2012

Summary
Cardio-facio-cutaneous (CFC) syndrome is caused by germ-line mutations in RAS, BRAF and MEK. The highly selective and potent MEK inhibitors that have been developed as anti-cancer agents hold potential as therapeutics for CFC syndrome. We have previously shown that the effects of CFC mutations on zebrafish gastrulation can be prevented by a one-hour treatment with MEK inhibitors within a specific developmental time-window. However, MEK activity is essential for normal development and PD0325901 treatment outside this treatment window leads to additional developmental defects in MEK dependent tissues. We now test 10 different doses of PD0325901 at six developmental time points and assess the effects on body axis length, heart development, and craniofacial structures in zebrafish embryos. Notably, we find that a continuous, partial dose of PD0325901 that has only minor inhibition of MEK activity can prevent the action of both the common CFC BRAFQ257R kinase-active allele and the BRAFG596V kinase-impaired mutant allele through the first five days of development. These results provide a detailed study of the effects of PD0325901 in development and show that, unlike in cancer that requires robust inhibition of MAPK signalling, a partial reduction in phospho-ERK activity treatment is sufficient to moderate the developmental effects BRAFCFC mutations.
Hydro-Mechanical and Chemical-Mineralogical Analyses of the Bentonite Buffer from A Full-Scale Field Experiment Simulating a High-Level Waste Repository
Authors: Dueck Ann , Johannesson Lars-Erik , Kristensson Ola , Olsson Siv , Sjöland Anders 
Published: February 2012

AbstractThe effect of exposure to repository-like conditions on compacted Wyoming bentonite was determined by comparing the hydraulic, mechanical, and mineralogical properties of samples from the bentonite buffer of the Canister Retrieval Test (CRT) with those of reference material. The CRT, located at the Swedish Äspö Hard Rock Laboratory (HRL), was a full-scale field experiment simulating conditions relevant for the Swedish, so called KBS-3, concept for disposal of high-level radioactive waste in crystalline host rock. The compacted bentonite, surrounding a copper canister equipped with heaters, had been subjected to heating at temperatures up to 95°C and hydration by natural Na-Ca-Cl type groundwater for almost 5 y at the time of retrieval.Under the thermal and hydration gradients that prevailed during the test, sulfate in the bentonite was redistributed and accumulated as anhydrite close to the canister. The major change in the exchangeable cation pool was a loss in Mg in the outer parts of the blocks, suggesting replacement of Mg mainly by Ca along with the hydration with groundwater. Close to the Cu canister, small amounts of Cu were incorporated into the bentonite. A reduction of strain at failure was observed in the innermost part of the bentonite buffer, but no influence was noted on the shear strength. No change in swelling pressure was observed, while a modest decrease in hydraulic conductivity was found for the samples with the highest densities. No coupling was found between these changes in the hydro-mechanical properties and the montmorillonite — the X-ray diffraction characteristics, the cation exchange properties, and the average crystal chemistry of the Na-converted <1 μm fractions provided no evidence of any chemical/structural changes in the montmorillonite after the 5 y hydrothermal test.
Polymer Model of Zeolite Thermochemical Stability
Authors: Arthur Randolph , Sasamoto Hiroshi , Walker Colin , Yui Mikazu 
Published: February 2012

AbstractThe polymer model provides a relatively simple and robust basis for estimating the standard Gibbs free energies of formation (ΔGfo) and standard enthalpies of formation (ΔHfo) of clay minerals and other aluminosilicates with an accuracy that is comparable to or better than can be obtained using alternative techniques. The model developed in the present study for zeolites entailed the selection of internally consistent standard thermodynamic properties for model components, calibration of adjustable model parameters using a linear regression technique constrained by ΔGfo and ΔHfo values retrieved from calorimetric, solubility, and phase-equilibrium experiments, and assessments of model accuracy based on comparisons of predicted values with experimental counterparts not included in the calibration dataset. The ΔGfo and ΔHfo predictions were found to average within ±0.2% and ±0.3%, respectively, of experimental values at 298.15 K and 1 bar. The latter result is comparable to the good accuracy that has been obtained by others using a more rigorous electronegativity-based model for ΔHfo that accounts explicitly for differences in zeolite structure based on differences in framework density and unit-cell volume. This observation is consistent with recent calorimetric studies indicating that enthalpies of transition from quartz to various pure-silica zeolite frameworks (zeosils) are small and only weakly dependent on framework type, and suggests that the effects on ΔHfo of differences in framework topology can be ignored for estimation purposes without incurring a significant loss of accuracy. The relative simplicity of the polymer model, together with its applicability to both zeolites and clay minerals, is based on a common set of experimentally determined and internally consistent thermodynamic properties for model components. These attributes are particularly well suited for studies of the effects of water-rock-barrier interactions on the long-term safety of geologic repositories for high-level nuclear waste (HLW).
Cost, Delay and Justice: The High Court of Australia Recognizes the Importance of Case Management in Civil Litigation— Aon Risk Services Australia Limited v Australian National University
Authors: Boniface Dorne , Legg Michael 
Published: February 2012

‘Justice’ in civil litigation has traditionally meant justice as between the parties. However, pressure on public resources and delay resulting from traditional civil procedures has precipitated reform that now requires judges to case manage proceedings. ‘Justice’ has been broadened by such reform to include taking into account cost, delay and prejudice to other users of the civil litigation system as a central consideration when determining whether to grant leave to amend. The High Court in Queensland v J L Holdings Pty Ltd appeared to maintain the traditional narrow concept of ‘justice’. Recently, however, the High Court appears to have, in part, resiled from that view when considering court rules concerning amendment. This article examines the High Court's interpretation of the court rules for amendment at issue in Aon Risk Services, the impact of that reasoning on the scope of J L Holdings and case management.
Barebacking and the ‘Cult of Violence’: Queering the Criminal Law
Authors: Ashford Chris 
Published: February 2012

This article seeks to revisit the law in relation to the sexual phenomenon of barebacking. Drawing upon queer theory, the article seeks to evaluate critically the development of the criminal law in relation to the practice of ‘unsafe’ sex by men with other men, known as barebacking, along with the broader casting of the judiciary as sexual custos mores. It will argue that the present heteronormative legal and cultural framework largely reflects a focus upon the ‘good gay’, de-sexed and constructed within a rights discourse, in contrast to Stychin's ‘bad queer’, sexual and defiant of a narrow heteronormative rights agenda, and embracing ‘unsafe’ and ‘deviant’ sexual practices. This article seeks to move the analysis of the criminal law on from the doctrinal debates that have dominated thus far, and onto a more theoretical exposition of the criminal law regarding barebacking as erotic play.
‘A Nod and a Wink’: Do ‘Gaming Practices' Provide an Insight into the Organisational Nature of Police Corruption?
Authors: Patrick Rodger 
Published: February 2012

Whether police corruption is an individual or an organisational phenomenon has been a feature of recent criminological debates. The definition of police corruption has also changed and more modern definitions, based on the motivation behind the behaviour, include perverse practices designed to give a false impression of improved performance. Such practices are referred to as ‘gaming’, and examples involving law enforcement agencies are regularly cited in the academic literature on this subject. In this article statistical patterns in police performance data are linked to particular forms of ‘gaming’ behaviour. It is argued that the scale and seismic nature of fluctuations linked to particular events, sometimes involving scandals or other exposures, indicate that the behaviour is organisational and linked to objectives being pursued by senior officers. The contributions of Her Majesty's Government Statistical Office and Home Office Research Development and Statistics department are acknowledged in the provision of the statistics on which this article is based.