bluuebunny/crossref_metadata_2025_split huggingface dataset:
Comparative Genomics of Two Closely Related Unicellular Thermo-Acidophilic Red Algae, Galdieria sulphuraria and Cyanidioschyzon merolae, Reveals the Molecular Basis of the Metabolic Flexibility of Galdieria sulphuraria and Significant Differences in Carbohydrate Metabolism of Both Algae
Authors: Barbier Guillaume , Oesterhelt Christine , Larson Matthew D. , Halgren Robert G. , Wilkerson Curtis , Garavito R. Michael , Benning Christoph , Weber Andreas P.M. 
Published: February 2005

Abstract
Unicellular algae serve as models for the study and discovery of metabolic pathways, for the functional dissection of cell biological processes such as organellar division and cell motility, and for the identification of novel genes and gene functions. The recent completion of several algal genome sequences and expressed sequence tag collections and the establishment of nuclear and organellar transformation methods has opened the way for functional genomics approaches using algal model systems. The thermo-acidophilic unicellular red alga Galdieria sulphuraria represents a particularly interesting species for a genomics approach owing to its extraordinary metabolic versatility such as heterotrophic and mixotrophic growth on more than 50 different carbon sources and its adaptation to hot acidic environments. However, the ab initio prediction of genes required for unknown metabolic pathways from genome sequences is not trivial. A compelling strategy for gene identification is the comparison of similarly sized genomes of related organisms with different physiologies. Using this approach, candidate genes were identified that are critical to the metabolic versatility of Galdieria. Expressed sequence tags and high-throughput genomic sequence reads covering &gt;70% of the G. sulphuraria genome were compared to the genome of the unicellular, obligate photoautotrophic red alga Cyanidioschyzon merolae. More than 30% of the Galdieria sequences did not relate to any of the Cyanidioschyzon genes. A closer inspection of these sequences revealed a large number of membrane transporters and enzymes of carbohydrate metabolism that are unique to Galdieria. Based on these data, it is proposed that genes involved in the uptake of reduced carbon compounds and enzymes involved in their metabolism are crucial to the metabolic flexibility of G. sulphuraria.
Benchmarking the CATMA Microarray. A Novel Tool forArabidopsis Transcriptome Analysis
Authors: Allemeersch Joke , Durinck Steffen , Vanderhaeghen Rudy , Alard Philippe , Maes Ruth , Seeuws Kurt , Bogaert Tom , Coddens Kathleen , Deschouwer Kirsten , Van Hummelen Paul , Vuylsteke Marnik , Moreau Yves , Kwekkeboom Jeroen , Wijfjes André H.M. , May Sean , Beynon Jim , Hilson Pierre , Kuiper Martin T.R. 
Published: February 2005

Abstract
Transcript profiling is crucial to study biological systems, and various platforms have been implemented to survey mRNAs at the genome scale. We have assessed the performance of the CATMA microarray designed for Arabidopsis (Arabidopsis thaliana) transcriptome analysis and compared it with the Agilent and Affymetrix commercial platforms. The CATMA array consists of gene-specific sequence tags of 150 to 500 bp, the Agilent (Arabidopsis 2) array of 60mer oligonucleotides, and the Affymetrix gene chip (ATH1) of 25mer oligonucleotide sets. We have matched each probe repertoire with the Arabidopsis genome annotation (The Institute for Genomic Research release 5.0) and determined the correspondence between them. Array performance was analyzed by hybridization with labeled targets derived from eight RNA samples made of shoot total RNA spiked with a calibrated series of 14 control transcripts. CATMA arrays showed the largest dynamic range extending over three to four logs. Agilent and Affymetrix arrays displayed a narrower range, presumably because signal saturation occurred for transcripts at concentrations beyond 1,000 copies per cell. Sensitivity was comparable for all three platforms. For Affymetrix GeneChip data, the RMA software package outperformed Microarray Suite 5.0 for all investigated criteria, confirming that the information provided by the mismatch oligonucleotides has no added value. In addition, taking advantage of replicates in our dataset, we conducted a robust statistical analysis of the platform propensity to yield false positive and false negative differentially expressed genes, and all gave satisfactory results. The results establish the CATMA array as a mature alternative to the Affymetrix and Agilent platforms.
Genome-Wide Annotation and Expression Profiling of Cell Cycle Regulatory Genes in Chlamydomonas reinhardtii
Authors: Bisova Katerina , Krylov Dmitri M. , Umen James G. 
Published: February 2005

Abstract
Eukaryotic cell cycles are driven by a set of regulators that have undergone lineage-specific gene loss, duplication, or divergence in different taxa. It is not known to what extent these genomic processes contribute to differences in cell cycle regulatory programs and cell division mechanisms among different taxonomic groups. We have undertaken a genome-wide characterization of the cell cycle genes encoded by Chlamydomonas reinhardtii, a unicellular eukaryote that is part of the green algal/land plant clade. Although Chlamydomonas cells divide by a noncanonical mechanism termed multiple fission, the cell cycle regulatory proteins from Chlamydomonas are remarkably similar to those found in higher plants and metazoans, including the proteins of the RB-E2F pathway that are absent in the fungal kingdom. Unlike in higher plants and vertebrates where cell cycle regulatory genes have undergone extensive duplication, most of the cell cycle regulators in Chlamydomonas have not. The relatively small number of cell cycle genes and growing molecular genetic toolkit position Chlamydomonas to become an important model for higher plant and metazoan cell cycles.
Medication errors in anaesthesia and critical care
Authors: Wheeler S. J. , Wheeler D. W. 
Published: February 2005

SummaryThere is an increasing recognition that medication errors are causing a substantial global public health problem, as many result in harm to patients and increased costs to health providers. However, study of medication error is hampered by difficulty with definitions, research methods and study populations. Few doctors are as involved in the process of prescribing, selecting, preparing and giving drugs as anaesthetists, whether their practice is based in the operating theatre, critical care or pain management. Anaesthesia is now safe and routine, yet anaesthetists are not immune from making medication errors and the consequences of their mistakes may be more serious than those of doctors in other specialties. Steps are being taken to determine the extent of the problem of medication error in anaesthesia. New technology, theories of human error and lessons learnt from the nuclear, petrochemical and aviation industries are being used to tackle the problem.
Effect‐site controlled patient maintained propofol sedation: a volunteer safety study*
Authors: Anderson K. J. , Leitch J. A. , Green J. S. , Kenny G. N. C. 
Published: February 2005

SummaryEffect‐site concentration is a mathematical term related to the clinical effect of a drug. We have designed a patient‐maintained sedation system for delivering propofol to the predicted effect‐site concentration rather than plasma concentration. To assess its efficacy and safety, 20 healthy volunteers deliberately attempted to over‐sedate themselves using the system. The new effect‐site concentration driven system delivered sedation successfully, and more rapidly than its predecessor. Fifteen volunteers ended the study when the system automatically reduced the effect‐site concentration after 6 min of no button presses despite verbal contact and maintenance of arterial oxygen saturation (at effect‐site concentration 1.8–3.8 μg.ml−1). Four out of 20 volunteers ended with minor arterial desaturation (lowest 88% at effect‐site concentration 2.6–3.4 μg.ml−1). One volunteer ended after loss of verbal contact at effect‐site concentration 3.4 μg.ml−1. Further modification of the system's design is necessary before it can be recommended for routine practice.
Nitrous oxide diffusion into the cuffs of disposable laryngeal mask airways
Authors: Maino P. , Dullenkopf A. , Bernet V. , Weiss M. 
Published: February 2005

SummaryThe aim of this study was to investigate cuff pressure changes found in disposable size 3 laryngeal mask airways (LMAs) from different manufacturers during nitrous oxide exposure and to compare the results with the re‐usable Classic LMA. In an in vitro experiment, laryngeal mask airway cuff pressures starting from a baseline pressure of 40 cm H2O were recorded using a pressure transducer for 60 min with the laryngeal mask airway cuff exposed to 66% N2O in oxygen. Cuff pressure increases within 5 min of nitrous oxide exposure were > 250% in the Classic LMA and were not significantly different from those found in the Marshall laryngeal mask airway. However, they were significantly greater than those in the Soft Seal, the Unique, the AMBU, and Intersurgical laryngeal mask airways, all of which demonstrated stable cuff pressure levels within the first 5 min. The cuff pressure increase following 60 min of nitrous oxide exposure was 13.0 ± 1.1 and 14.6 ± 0.7 cm H2O in the Intersurgical and Unique laryngeal mask airways, respectively, which was significantly lower than the cuff pressure increase in the Soft Seal and in the Ambu laryngeal mask airways (28.3 ± 2.9 and 30.9 ± 1.2 cm H2O, respectively). Unlike the re‐usable Classic LMA and the disposable Marshall laryngeal mask airway, which have silicone cuffs, the disposable Ambu, Intersurgical, Portex Soft Seal and Unique laryngeal mask airways have cuffs constructed from PVC, which seems to be less susceptible to hyperinflation caused by nitrous oxide diffusion.
Psychometric characteristics of simulation‐based assessment in anaesthesia and accuracy of self‐assessed scores*
Authors: Weller J. M. , Robinson B. J. , Jolly B. , Watterson L. M. , Joseph M. , Bajenov S. , Haughton A. J. , Larsen P. D. 
Published: February 2005

SummaryThe purpose of this study was to define the psychometric properties of a simulation‐based assessment of anaesthetists. Twenty‐one anaesthetic trainees took part in three highly standardised simulations of anaesthetic emergencies. Scenarios were videotaped and rated independently by four judges. Trainees also assessed their own performance in the simulations. Results were analysed using generalisability theory to determine the influence of subject, case and judge on the variance in judges' scores and to determine the number of cases and judges required to produce a reliable result. Self‐assessed scores were compared to the mean score of the judges. The results suggest that 12–15 cases are required to rank trainees reliably on their ability to manage simulated crises. Greater reliability is gained by increasing the number of cases than by increasing the number of judges. There was modest but significant correlation between self‐assessed scores and external assessors' scores (rho = 0.321; p = 0.01). At the lower levels of performance, trainees consistently overrated their performance compared to those performing at higher levels (p = 0.0001).
Transient fixation on a non‐native language associated with anaesthesia
Authors: Webster C. S. , Grieve R. O. S. 
Published: February 2005

SummaryWe report a patient with the unusual language disturbance of transient fixation on a non‐native language after otherwise uneventful general anaesthesia. The patient was unable to speak his native language for a period of 5–10 min, despite a desire to do so. He fully and spontaneously recovered from the episode. The phenomenon raises a number of interesting questions about the nature of human language, anaesthesia and consciousness. We discuss our patient in the context of some of these questions and present a review of three similar patients reported in the anaesthetic literature.
Flow cytometric investigation of peri‐anaesthetic anaphylaxis using CD63 and CD203c
Authors: Sudheer P. S. , Hall J. E. , Read G. F. , Rowbottom A. W. , Williams P. E. 
Published: February 2005

SummaryThe investigation of anaphylactic reactions in the peri‐operative period is difficult. Elevation of serum tryptase levels is a good indicator of an anaphylactic event but the ability of subsequent investigations to identify the drug(s) responsible for the reaction is still potentially unreliable. The aim of this study was to examine basophil activation as an investigative tool. We performed flow cytometric analysis of the expression on the cell surface of the basophil activation markers CD63 and CD203c and measured histamine release in 21 patients who were referred with possible peri‐operative anaphylaxis. The sensitivity of CD63, CD203c, basophil histamine release and skin prick for the muscle relaxants was found to be 79%, 36%, 36% and 64%, respectively; the specificity was found to be 100%. These results demonstrate the difficulty in investigating the cause of an unexpected clinical event following drug administration, but the higher sensitivity of neo‐expression on the cell surface of CD63 suggests that flow cytometric analysis of its neo‐expression on basophils in vitro may be a diagnostic aid.
SNAP index and Bispectral index during different states of propofol/remifentanil anaesthesia*
Authors: Schmidt G. N. , Bischoff P. , Standl T. , Lankenau G. , Hellstern A. , Hipp C. , Schulte am Esch J. 
Published: February 2005

SummaryThe accuracy of the new SNAP index with the Bispectral index (BIS) to distinguish different states of propofol/remifentanil anaesthesia was compared in 19 female patients who were undergoing minor gynaecological surgery. Comparisons of the SNAP index, BIS, spectral edge frequency, mean arterial blood pressure and heart rate were performed. The ability of all parameters to distinguish between the steps of anaesthesia –awake vs. loss of response, awake vs. anaesthesia, anaesthesia vs. first reaction and anaesthesia vs. extubation – were analysed with the prediction probability. The prediction probability to differentiate between two interesting nuances of anaesthetic states –loss of response vs. first reaction – was calculated. Only the BIS showed no overlap between the investigated steps of anaesthesia. Both the SNAP index and BIS failed to differentiate the nuances of anaesthesia. The SNAP index and BIS were superior to mean arterial blood pressure and heart rate and spectral edge frequency in distinguishing between different steps of anaesthesia with propofol and remifentanil and provided useful additional information.
Drug error in anaesthetic practice: a review of 896 reports from the Australian Incident Monitoring Study database
Authors: Abeysekera A. , Bergman I. J. , Kluger M. T. , Short T. G. 
Published: February 2005

SummaryEight hundred and ninety‐six incidents relating to drug error were reported to the Australian Incident Monitoring Study. Syringe and drug preparation errors accounted for 452 (50.4%) incidents, including 169 (18.9%) involving syringe swaps where the drug was correctly labelled but given in error, and 187 (20.8%) due to selection of the wrong ampoule or drug labelling errors. The drugs most commonly involved were neuromuscular blocking agents, followed by opioids. Equipment misuse or malfunction accounted for a further 234 (26.1%) incidents; incorrect route of administration 126 (14.1%) incidents; and communication error 35 (3.9%) incidents. The outcomes of these events included minor morbidity in 105 (11.7%), major morbidity in 42 (4.7%), death in three (0.3%) and awareness under anaesthesia in 40 (4.4%) incidents. Contributing factors included inattention, haste, drug labelling error, communication failure and fatigue. Factors minimising the events were prior experience and training, rechecking equipment and monitors capable of detecting the incident. The information gained suggests areas where improved guidelines are required to reduce the incidence of drug error. Further research is required into the effectiveness of preventive strategies.
Repeatability enhancement in deep‐water permanent seismic installations: a dynamic correction for seawater velocity variations
Authors: Bertrand Alexandre , MacBeth Colin 
Published: February 2005

ABSTRACTWith the increasing use of permanently installed seismic installations, many of the issues in time‐lapse seismic caused by the lack of repeatability can be reduced. However, a number of parameters still influence the degree of reliability of 4D seismic data. In this paper, the specific impact of seawater velocity variations on time‐lapse repeatability is investigated in a synthetic study. A zero‐lag time‐lapse seabed experiment with no change in the subsurface but with velocity changes in the water column is simulated. The velocity model in the water column is constant for the baseline survey while the model for the repeat survey is heterogeneous, designed from sea salinity and temperature measurements in the West of Shetlands. The difference section shows up to 80% of residual amplitude, which highlights the poor repeatability. A new dynamic correction which removes the effect of seawater velocity variations specifically for permanent installations is developed. When applied to the synthetic data, it reduces the difference residual amplitude to about 3%. This technique shows substantial improvement in repeatability beyond conventional time‐lapse cross‐equalization.
Rock physics analysis for time‐lapse seismic at Schiehallion Field, North Sea
Authors: Meadows Mark , Adams Don , Wright Rich , Tura Ali , Cole Steve , Lumley David 
Published: February 2005

ABSTRACTRock physics analysis plays a vital role in time‐lapse seismic interpretation because it provides the link between changes in rock and fluid properties and the resulting seismic data response. In this case study of the Schiehallion Field, we discuss a number of issues that commonly arise in rock physics analyses for time‐lapse studies. We show that:

Logarithmic fits of dry bulk (Kdry) and shear (Gdry) moduli vs. effective pressure (Peff) are superior to polynomial fits.
2D surface fits of Kdry and Gdry over porosity (φ) and effective pressure using all the core data simultaneously are more useful and accurate than separate 1D fits over φ and Peff for each individual core.
One average set (facies) of Kdry(φ, Peff) and Gdry(φ, Peff) can be chosen to represent adequately the entire Schiehallion reservoir.
Saturated velocities and densities modelled by fluid substitution of Kdry(φ, Peff), Gdry(φ, Peff) and the dry bulk density ρdry(φ) compare favourably with well‐log velocities and densities.
P‐ and S‐wave impedance values resulting from fluid substitution of Kdry(φ, Peff), Gdry(φ, Peff) and ρdry(φ) show that the largest impedance changes occur for high porosities and low effective pressures.
Uncertainties in Kdry(φ, Peff) and Gdry(φ, Peff) derived for individual cores can be used to generate error surfaces for these moduli that represent bounds for quantifying uncertainties in seismic modelling or pressure–saturation inversion.
4D seismic for oil‐rim monitoring
Authors: Staples Rob , Hague Paul , Weisenborn Toon , Ashton Peter , Michalek Barbara 
Published: February 2005

ABSTRACTIn the central North Sea ‘Gannet‐A’ field, a 50 ft oil rim is overlain by a gas cap of variable thickness. Oil is produced from horizontal wells which initially produced dry oil, but as the field became more mature, a significant water cut was seen in several wells. A dedicated 4D seismic monitor survey was acquired in order to assess the remaining distribution of oil reserves. By forward modelling the synthetic seismic response to parameters such as contact movement and residual saturations (using 2D and 3D wedge models), and comparing the results with real seismic data, we are able to decipher the contact movements across the field. It is shown that, in one part of the field, the increased water cut is caused primarily by the vertical displacement of the entire oil rim into the initial gas cap. This oil‐rim displacement produces a very different 4D seismic response from the case of a static gas–oil contact and rising oil–water contact (normal production). As a result of these observations, we are able to optimize field production by both re‐perforation of existing wells and by drilling sidetracks into the displaced rim: a brown‐field development opportunity that might otherwise be missed.
4D technology: where are we, and where are we going?
Authors: Calvert Rodney 
Published: February 2005

ABSTRACT4D reservoir monitoring is now becoming established as a normal part of business in some companies, in some regions such as the North Sea, and for some applications, such as thermally enhanced oil recovery. Some spectacular technical successes have been reported, mostly in monitoring water floods. We are beginning to understand how to acquire and process surveys to achieve good results. There is still, however, much to improve in how we use 4D technology to capture its potential value in field management and still some way to go in the tool itself, to make it faster, cheaper and more sensitive to small production effects.
Cross‐matching with interpreted warping of 3D streamer and 3D ocean‐bottom‐cable data at Valhall for time‐lapse assessment
Authors: Hall Stephen A. , MacBeth Colin , Barkved Olav I. , Wild Philip 
Published: February 2005

ABSTRACTLegacy streamer data and newer 3D ocean‐bottom‐cable data are cross‐matched and analysed for time‐lapse analysis of geomechanical changes due to production in the Valhall Field. The issues relating to time‐lapse analysis using two such distinctly different data sets are addressed to provide an optimal cross‐matching workflow that includes 3D warping. Additionally an assessment of the differences between the imaging using single‐azimuth streamer and multi‐azimuth ocean‐bottom‐cable data is provided. The 3D warping utilized in the cross‐matching procedure is sensitive to acquisition and processing differences but is also found to provide valuable insight into the geometrical changes that occur in the subsurface due to production. As such, this work also provides a demonstration of the use of high‐resolution 3D interpreted warping to resolve the 3D heterogeneity of the compaction and subsidence. This is an important tool for Valhall, and possibly other fields, where compaction and subsidence (and monitoring thereof) are key factors in the reservoir management since the predominant observed production‐induced changes are compaction of the soft, high‐porosity chalk reservoir, due to pore‐pressure reduction, and the resultant overburden subsidence. Such reservoir compaction could have significant implications for production by changing permeabilities and production rates. Furthermore the subsidence effects could impact upon subsea installations and well‐bore stability. Geomechanical studies that have previously been used to model such subsidence and compaction are only constrained by observed surface displacements and measured reservoir pressure changes, with the geological overburden being largely neglected. The approaches suggested herein provide the potential for monitoring and assessment in three dimensions, including the probable heterogeneity and shearing, that is needed for full understanding of reservoir compaction and the resultant effects on the overburden to, for example, mitigate well‐bore failures.