bluuebunny/crossref_metadata_2025_split huggingface dataset:
Modeling drifting snow in Antarctica with a regional climate model: 2. Results
Authors: Lenaerts J. T. M. , van den Broeke M. R. 
Published: January 2012

This paper presents a model study of the impact of drifting snow on the lower atmosphere, surface snow characteristics, and surface mass balance of Antarctica. We use the regional atmospheric climate model RACMO2.1/ANT with a high horizontal resolution (27 km), equipped with a drifting snow routine and forced by ERA‐Interim (1989–2009) at its lateral and ocean boundaries. Drifting snow sublimation (SUds) is significant in Antarctica, especially in the coastal regions (>150 mm water equivalent yr−1). Integrated over the ice sheet, SUds removes ∼6% of the annually precipitated snow. Drifting snow interacts with the atmosphere, as it increases the lower atmospheric moisture content and reduces surface sublimation (SUs), and leads to increased snowfall in regions where the atmosphere usually is close to saturation. Drifting snow sublimation (SUds) is smallest in summer, when katabatic wind speeds are lower and melting and surface sublimation consolidate the snow surface. Compared to a simulation without drifting snow, total sublimation (SUds + SUs) doubles on the grounded ice sheet if drifting snow is considered. Drifting snow erosion is locally significant, but can be neglected on a continent‐wide scale.
Winter sea‐ice melt in the Canada Basin, Arctic Ocean
Authors: Jackson Jennifer M. , Williams William J. , Carmack Eddy C. 
Published: January 2012

Recent warming and freshening of the Canada Basin has led to the year‐round storage of solar radiation as the near‐surface temperature maximum (NSTM). Using year‐round ocean (from ice tethered profilers and autonomous ocean flux buoys), sea‐ice (from ice mass balance buoys), and atmosphere (from NCEP/NCAR reanalysis) data from 2005–2010, we find that heat from the NSTM is entrained into the surface mixed layer (SML) during winter. Entrainment can only occur when the base of the SML reaches the top of the NSTM. If this condition is met, the surface forcing and stratification together determine whether the SML deepens into the NSTM. Heat transfer occurs by diffusion or by the erosion of the summer halocline. The average temperature of the SML warmed by as much as 0.06°C during storm events. Solar radiation began warming the SML about 1 month early during the winter of 2007–2008 and this can be explained by thin sea ice.
Assimilation of passive and active microwave soil moisture retrievals
Authors: Draper C. S. , Reichle R. H. , De Lannoy G. J. M. , Liu Q. 
Published: January 2012

Near‐surface soil moisture observations from the active microwave ASCAT and the passive microwave AMSR‐E satellite instruments are assimilated, both separately and together, into the NASA Catchment land surface model over 3.5 years using an ensemble Kalman filter. The impact of each assimilation is evaluated using in situ soil moisture observations from 85 sites in the US and Australia, in terms of the anomaly time series correlation‐coefficient, R. The skill gained by assimilating either ASCAT or AMSR‐E was very similar, even when separated by land cover type. Over all sites, the mean root‐zone R was significantly increased from 0.45 for an open‐loop, to 0.55, 0.54, and 0.56 by the assimilation of ASCAT, AMSR‐E, and both, respectively. Each assimilation also had a positive impact over each land cover type sampled. For maximum accuracy and coverage it is recommended that active and passive microwave observations be assimilated together.
Neutral thermospheric dynamics observed with two scanning Doppler imagers: 2. Vertical winds
Authors: Anderson C. , Conde M. , McHarg M. G. 
Published: January 2012

This article is the second in a series of three papers reporting on observations of the 630.0 nm thermospheric airglow emission by two spatially separated scanning Doppler imagers (SDI’s) in Alaska. In this article, line‐of‐sight wind measurements from these instruments in four common‐volume regions lying along the great circle joining the two observatories have been used to derive estimates of the vertical wind in those common‐volumes. These estimates are combined with the vertical winds measured directly in each of the station zeniths to resolve both the spatial and temporal variations of the vertical wind field. Data from four nights are presented as examples of the wave‐like oscillations and frequently high spatial correlations that are observed. A statistical study of data from the full 19‐night data set showed that the frequency of observing statistically significant correlation between vertical winds measured at separate locations decreased linearly with increasing separation. A linear fit to this trend indicated that for this particular location and orientation the largest separation over which statistically significant correlation would be expected to occur is approximately 540 km.
Polarization of Pc1/EMIC waves and related proton auroras observed at subauroral latitudes
Authors: Nomura R. , Shiokawa K. , Sakaguchi K. , Otsuka Y. , Connors M. 
Published: January 2012

We have investigated the polarization of Pc1 geomagnetic pulsations and related proton auroras at subauroral latitudes, using an induction magnetometer and an all‐sky camera at Athabasca, Canada (54.7°N, 246.7°E, magnetic latitude (mlat) 61.7°N). Isolated proton auroras often appear in association with Pc1 pulsations, because of proton scattering by electromagnetic ion cyclotron (EMIC) waves in the magnetosphere. We used the proton aurora as a proxy for the location and size of the Pc1 ionospheric source. For 27 Pc1 events with simultaneously observed proton auroras over 4 years from September 7, 2005 to September 6, 2009, we calculated the distances between the Pc1 ionospheric source and the observation site, normalized by the scale size of the source. We tried three different definitions of the scale size of Pc1 ionospheric source to calculate the normalized distances. We found that the rotation angleθ between the Pc1 polarization ellipse and the direction to the proton aurora changes from 90° to 0° as the normalized distance increases. For the definition of the scale sizes that gives most clear θ‐transition from 90° to 0°, the transition occurs at the normalized distance ∼2.0–4.0, while it was ∼1.0–2.0 by the model calculation of Fujita and Tamao (1988). The averaged major axes tend to point toward the proton aurora at larger distances. The difference of the transition location may imply that the Pc1 ionospheric sources are larger than the isolated proton auroras, or that the inhomogenuity of the ionospheric conductivity by the proton precipitation affects the transition distances.
Numerical investigation of the quasi 2 day wave in the mesosphere and lower thermosphere
Authors: Yue Jia , Liu Han‐Li , Chang Loren C. 
Published: January 2012

The zonal wave number 3 planetary wave with about a 2 day period is a recurrent wave feature in the mesosphere and lower thermosphere (MLT). The quasi 2 day wave (QTDW) exhibits strong seasonal variability with peak amplitudes after summer solstice. In late January and early February, satellites also discovered two strong enhancements of the QTDW in meridional wind, one peak at summer midlatitudes near 90 km and the other in the tropical lower thermosphere. For the first time, this double‐peak characteristic of the QTDW meridional component is numerically investigated by the National Center for Atmospheric Research (NCAR) thermosphere‐ionosphere‐mesosphere‐electrodynamics general circulation model (TIME‐GCM) with the QTDW forcing prescribed at the lower model boundary and explained by the combined effect of baroclinic‐barotropic instability and Rossby normal mode. Baroclinic‐barotropic instability is capable of amplifying the QTDW, manifesting as Eliassen‐Palm (EP) flux divergence in the summer mesosphere. Without the direct contribution from baroclinic‐barotropic instability, the simulated QTDW response in a lower thermosphere temperature and horizontal wind resembles that of the (3, 0) Rossby‐gravity normal mode. In the summer middle atmosphere, the wave amplitude grows substantially, like an internal wave in the regions of large refractive index. As the wave amplitude growth ceases near the mesopause, where the zonal wind reverses direction, the QTDW reaches its maximum amplitude, displaying an enhanced meridional component in the tropical lower thermosphere. Several new aspects on the QTDWs in the MLT were also revealed. Compared with a prior model run, the propagation of the QTDW can also be prohibited by a self‐generated critical layer in a strong thermospheric easterly wind. In addition, a direct contribution from the migrating diurnal tide to the QTDW amplitude in the MLT is found. This is largely attributed to the change of the background zonal wind caused by the tide, thus leading to the increase of the QTDW refractive index in the summer middle atmosphere.
Plasmodium falciparum has rare correlation properties
Authors: Shah Kushal 
Published: January 2012

AbstractA plot of the correlation function of a given DNA sequence has certain characteristic features common to almost all organisms. One common feature is that the correlation values at distances that are multiples of three is higher than correlation values at other distances. Because of this such a correlation plot can be divided into two or three curves with different scalings. P. falciparum has a rare correlation property which is probably unique. I have analyzed genomes of many bacteria, fungi and protozoa and found that P. falciparum is the only organism whose DNA sequence correlation plot can be divided into four curves with different scalings. This property is neither shared by other species of the Plasmodium genus nor by other AT rich genomes. This could be a hint that the DNA sequence of P. falciparum has undergone certain rare mutational events.
Regulation of human microsomal prostaglandin E synthase-1 by IL-1β requires a distal enhancer element with a unique role for C/EBPβ
Authors: Walters Jewell N. , Bickford Justin S. , Newsom Kimberly J. , Beachy Dawn E. , Barilovits Sarah J. , Herlihy John-David , Nick Harry S. 
Published: January 2012

The studies of PGE2 (prostaglandin E2) biosynthesis have focused primarily on the role of cyclo-oxygenases. Efforts have shifted towards the specific PGE2 terminal synthases, particularly mPGES-1 (microsomal PGE synthase 1), which has emerged as the crucial inducible synthase with roles in pain, cancer and inflammation. mPGES-1 is induced by pro-inflammatory cytokines with studies focusing on the proximal promoter, mediated specifically through Egr-1 (early growth-response factor 1). Numerous studies demonstrate that the mPGES-1 promoter (PTGES) alone cannot account for the level of IL-1β (interleukin 1β) induction. We identified two DNase I-hypersensitive sites within the proximal promoter near the Egr-1 element and a novel distal site near −8.6 kb. Functional analysis of the distal site revealed two elements that co-operate with basal promoter expression and a stimulus-dependent enhancer. A specific binding site for C/EBPβ (CCAAT/enhancer-binding protein β) in the enhancer was directly responsible for inducible enhancer activity. ChIP (chromatin immunoprecipitation) analysis demonstrated constitutive Egr-1 binding to the promoter and induced RNA polymerase II and C/EBPβ binding to the promoter and enhancer respectively. Knockout/knockdown studies established a functional role for C/EBPβ in mPGES-1 gene regulation and the documented interaction between Egr-1 and C/EBPβ highlights the proximal promoter co-operation with a novel distal enhancer element in regulating inducible mPGES-1 expression.
The development of the BSAC standardized method of disc diffusion testing
Authors: Andrews Jennifer M. 
Published: January 2012

Abstract
The BSAC Working Party on Susceptibility Testing has developed a standardized method of disc susceptibility testing that has been ‘field tested’ in 19 diagnostic laboratories in the UK and Ireland. The method employs semi-defined media, a semi-confluent inoculum and relates zones of inhibition with BSAC-specified MIC breakpoints to interpret susceptibility. The bacteria selected for the trial included clinical isolates and control strains from the ATCC and NCTC national collections. Organisms were chosen because they had known attributes, such as being fully susceptible or having a demonstrated mechanism of resistance. The results from this survey are very encouraging. With the commonly isolated Enterobacteriaceae, specifically Escherichia coli, Proteus mirabilis and Klebsiella spp., no major problems were observed except with gentamicin and cefuroxime. In the case of gentamicin, problems were associated with resistant strains of P. mirabilis, with MICs of 2 mg/L, being falsely reported as susceptible. For cefuroxime, it is not unexpected that results were unreliable, as the MIC distribution straddles the in vitro breakpoint concentration (following the results of this study the MIC and zone diameter breakpoints have been amended to improve reporting). No major problems were encountered for Pseudomonas aeruginosa with the agents studied. The ‘field survey’ has shown that disc testing is unreliable for determining the susceptibility of coagulase-negative staphylococci to teicoplanin, and that the detection of glycopeptide resistance in enterococci is improved by incubation for a full 24 h. Inconsistencies observed with fastidious organisms were associated with incorrect inocula. Zone diameter data for the control strains studied provide information that can be utilized by diagnostic laboratories to monitor the daily performance of testing.
BSAC standardized disc susceptibility testing method
Authors:   for the BSAC Working Party on Susceptibility Testing, Andrews Jennifer M. 
Published: January 2012

Abstract
For nearly a decade microbiologists have used the MIC breakpoints published in the BSAC Guide to Susceptibility Testing to interpret susceptibility. Historically, and unlike the rest of Europe, the UK and Ireland have used a comparative method of disc testing to interpret susceptibility rather than one based on a correlation between MIC and zone of inhibition. Although innovative when introduced in the 1970s, Stokes' comparative method has evolved ad hoc and it has become increasingly apparent that there is a need for a standardized method of disc testing that is correlated with BSAC MIC breakpoints. The method described here, like all other standardized methods of disc testing, cannot be adapted by the user, and interpretative criteria are only applicable if the method is adhered to fully. A major advantage of this approach to susceptibility testing is that data from several sources can be combined for surveillance of resistance, a task that has been made much easier by the introduction of this method and coincides with the availability of automated zone measuring devices. It is hoped that the method described here will provide the core document for standard operating procedures; however, changes will necessarily occur over time as the method is developed and refined.
Determination of minimum inhibitory concentrations
Authors: Andrews Jennifer M. 
Published: January 2012

Abstract
Minimum inhibitory concentrations (MICs) are defined as the lowest concentration of an antimicrobial that will inhibit the visible growth of a microorganism after overnight incubation, and minimum bactericidal concentrations (MBCs) as the lowest concentration of antimicrobial that will prevent the growth of an organism after subculture on to antibiotic-free media. MICs are used by diagnostic laboratories mainly to confirm resistance, but most often as a research tool to determine the in vitro activity of new antimicrobials, and data from such studies have been used to determine MIC breakpoints. MBC determinations are undertaken less frequently and their major use has been reserved for isolates from the blood of patients with endocarditis. Standardized methods for determining MICs and MBCs are described in this paper. Like all standardized procedures, the method must be adhered to and may not be adapted by the user. The method gives information on the storage of standard antibiotic powder, preparation of stock antibiotic solutions, media, preparation of inocula, incubation conditions, and reading and interpretation of results. Tables giving expected MIC ranges for control NCTC and ATCC strains are also supplied.
Quality assurance of antimicrobial susceptibility testing by disc diffusion
Authors: King Anna , Brown Derek F. J. 
Published: January 2012

Abstract
Quality assurance is essential to ensure the quality of antimicrobial susceptibility tests by diffusion methods. Routine internal quality control testing with a range of control strains is a major part of the quality assurance process, as it facilitates monitoring of the performance of the test. Most standardized methods include tables of acceptable zone size ranges for control strains and, in addition to checking that control zone diameters are within the published ranges, rules or statistical approaches may be applied to indicate deviations from acceptable performance. If control tests indicate unacceptable performance, the source(s) of the error should be investigated and may include problems with media, antimicrobial discs, inoculum and plate reading. Participation in external quality assessment schemes provides an independent assessment of performance although the number of strains distributed in such schemes is limited. Internal quality assessment in which routine tests are repeated with the identity of the organisms blinded is a useful complementary approach to external quality assessment and may detect problem areas not highlighted by other control methods. Education is an important part of the quality assurance process. Knowledge of atypical results for different organism–agent combinations may provide warning of possibly erroneous results, and an understanding of the limitations and sources of error in disc diffusion methods contributes significantly to the recognition, resolution and avoidance of errors.
Instrumentation in antimicrobial susceptibility testing
Authors: Felmingham David , Brown Derek F. J. 
Published: January 2012

Abstract
Studies in the 1960s demonstrated the problems of variability in susceptibility testing methods, especially those affecting the performance of disc diffusion procedures. These studies made apparent the need for standardization and resulted in more clearly defined performance limits for growth medium, incubation conditions, inoculum concentration, disc content for diffusion methods, the setting of interpretative MIC breakpoints and the establishment of quality control parameters. More recently, there has been a growing interest in the use of instrumentation for reading disc diffusion tests and the endpoints of agar or broth dilution MIC determinations. Instrumentation ranges in complexity from the simple optical reading of zones of inhibition or growth endpoints, requiring operator interpretation, to more sophisticated devices for reading, recording and ‘expert system’ analysis of results with interfacing of instruments to laboratory information management systems. Some of the more developed systems are fully automated and can also identify the organisms tested. The pressure to reduce labour costs and provide results earlier favours the use of more automated systems whilst the requirement for resistance surveillance provides impetus for the use of systems that provide quantitative results and electronic data handling.
Interpretative reading: recognizing the unusual and inferring resistance mechanisms from resistance phenotypes
Authors: Livermore David M. , Winstanley Trevor G. , Shannon Kevin P. 
Published: January 2012

Abstract
If isolates are speciated and if a sufficient range of antibiotics is tested, underlying resistance mechanisms can often be inferred from the antibiogram data. This allows: (i) anomalous combinations of phenotype and organism to be reconsidered; (ii) prediction of further antibiotics that deserve testing; and (iii) the suppression of susceptibilities that are anomalous in the light of the inferred mechanism. This ‘interpretative reading’ is widely undertaken in France but is largely precluded in the UK by limited speciation and the testing of narrow ranges of antibiotics. Nevertheless, UK laboratories should be aware of: (i) grossly anomalous combinations of species and phenotype, demanding reference laboratory confirmation; (ii) useful indicator drugs, where resistance implies a mechanism conferring other resistances that may be less obvious in direct tests; and (iii) antibiotics that are prone to select resistant mutants of particular species during therapy. Details of these combinations of organism and resistance are presented. Relationships between antibiogram and mechanism are also presented to allow full interpretative reading for those testing wide panels of drugs versus speciated isolates.
Preface
Authors: Barnes Rosemary A. , Johnson Elizabeth M. , Odds Frank C. 
Published: January 2012

Abstract
The clinical problems caused by life-threatening, deeptissue fungal infections affect many different medical and surgical specialities where immunosuppression through disease or therapeutic advance has created a substantial sub-category of patients at risk of mycosis. Amphotericin B remains one of the first-line agents for treatment of almost all systemic mycoses, but the agent in its conventional deoxycholate formulation carries a serious penalty in terms of nephrotoxicity. Novel, lipid-associated formulations of amphotericin B have been introduced to combat the toxicity problem without loss of therapeutic efficacy.
This supplement is based upon papers presented at an international symposium held in Australia on 8–9 July 2000. It focuses on AmBisome, a liposome-encapsulated formulation of amphotericin B, and draws together information on many general aspects of the diagnosis and treatment of deep tissue mycoses as well as providing a comprehensive set of reviews of all aspects of AmBisome —its pharmacology, toxicology, pharmacokinetics and clinical efficacy in a variety of mycoses and patient types. There is now considerably more clinical experience with lipid forms of amphotericin B than when the previous supplement on AmBisome was published by the Journal of Antimicrobial Chemotherapy in October 1999.1
Because the topic of the supplement is a formulation of an antifungal agent, not the agent itself, and because lipid-based formulations can vary in composition even when they are nominally prepared in the same way, we have taken the unusual step of referring to the various amphotericin B lipid formulations, and to ‘conventional’ amphotericin B-deoxycholate for injection, by their trade names.
The editors would like to thank Christine Burley of the JAC Editorial Office, and Regine Buffels of Gilead Sciences for their untiring support and assistance in the preparation of this supplement.
Reference
1. Speller, D. C. E. & Warnock, D. W. (Eds). (1991). Liposomal amphotericin B (AmBisome) in the treatment of systemic fungal infection. Journal of Antimicrobial Chemotherapy28, Suppl. B, 1–118.