bluuebunny/crossref_metadata_2025 huggingface dataset:
Global simulations of ice nucleation and ice supersaturation with an improved cloud scheme in the Community Atmosphere Model
Authors: Gettelman A. , Liu X. , Ghan S. J. , Morrison H. , Park S. , Conley A. J. , Klein S. A. , Boyle J. , Mitchell D. L. , Li J.‐L. F.
Published: September 2010

A process‐based treatment of ice supersaturation and ice nucleation is implemented in the National Center for Atmospheric Research Community Atmosphere Model (CAM). The new scheme is designed to allow (1) supersaturation with respect to ice, (2) ice nucleation by aerosol particles, and (3) ice cloud cover consistent with ice microphysics. The scheme is implemented with a two‐moment microphysics code and is used to evaluate ice cloud nucleation mechanisms and supersaturation in CAM. The new model is able to reproduce field observations of ice mass and mixed phase cloud occurrence better than previous versions. The model is able to reproduce observed patterns and frequency of ice supersaturation. Simulations indicate homogeneous freezing of sulfate and heterogeneous freezing on dust are both important ice nucleation mechanisms, in different regions. Simulated cloud forcing and climate is sensitive to different formulations of the ice microphysics. Arctic surface radiative fluxes are sensitive to the parameterization of ice clouds. These results indicate that ice clouds are potentially an important part of understanding cloud forcing and potential cloud feedbacks, particularly in the Arctic.
Flow resistance in steep streams: An experimental study
Authors: Zimmermann André
Published: September 2010

Frequently, an assessment of the mean water velocity in a stream is necessary to estimate the discharge associated with a particular flow depth or, conversely, the mean depth associated with a particular discharge. In the absence of a direct measurement of flow velocity, a flow resistance approach, which establishes the relation between depth and velocity, can be applied. Two approaches have been used in the past: traditional approaches based on the use of a resistance coefficient (e.g., Darcy‐Weisbach) or dimensionless hydraulic geometry approaches. To examine if one approach is more appropriate for steep streams, data from 31 flume experiments conducted to examine flow resistance in self‐formed cascade channels were analyzed. A dimensionless hydraulic geometry approach developed using at‐a‐station data to characterize the q* exponent and between‐site data to characterize the exponent on the channel slope term was more accurate than more traditional approaches. The developed relation was similar to the established rational relation (v α g0.2q0.6s−0.4S0.2), suggesting that the rational relation has merit. The approach does not utilize a flow partitioning approach since, in steep streams with small relative depths, the grains themselves generate form and spill resistance. The observation that a single dimensionless hydraulic geometry flow resistance relation can describe measurements across a range of grain sizes and bed slopes (3–21%) suggests that steep streams may follow a single scaling relation similar to the regime equations associated with lowland rivers.
Assessing the skill of satellite‐based precipitation estimates in hydrologic applications
Authors: Pan Ming , Li Haibin , Wood Eric
Published: September 2010

An important application of global precipitation measurement rainfall products is providing forcing inputs for hydrologic applications, and the goal of this study is to assess how skillful they are for such applications. To do that, we force a land surface model with both satellite estimates and ground‐based measurements and test how well they can predict hydrologic states and fluxes useful for water resource applications, i.e., soil moisture, evapotranspiration, and river streamflow. A number of satellite‐based precipitation products ranging from retrievals based only on microwave measurements, combined microwave + infrared estimates, to gauge‐corrected products are tested over the entire continental United States region. As a reference to the satellite retrievals, estimates from global and regional weather model reanalyses (the analysis fields from these models) are tested as well. It is found that the microwave + infrared combined estimates can match the skill of the coarse resolution European Center for Medium‐Range Weather Forecasts global reanalysis but not the regional National Center for Environmental Predictions reanalysis. Gauge corrections to satellite products significantly enhance their skill by greatly reducing the bias in hydrologic predictions, especially over mountainous areas. Rainfall errors are shown to have strong impact on river streamflow predictions and column total soil moisture and relatively weak impact on near surface moisture and evapotranspiration. River streamflow experiments also suggest that satellite rainfall errors are highly correlated in space within the range of one storm system and thus do not reduce in magnitude with spatial scale (basin size).
Impact of meteorological factors on the correlation between aerosol optical depth and cloud fraction
Authors: Engström Anders , Ekman Annica M. L.
Published: September 2010

The aerosol optical depth has in several recent studies been found to correlate with cloud fraction. This study examines the global distribution of the total correlation between aerosol optical depth, cloud fraction and meteorological conditions using satellite observations together with atmospheric re‐analysis data from the ECMWF. The results show large regional differences in the correlation between aerosol optical depth and cloud fraction, where a higher correlation is found over remote ocean. The one meteorological variable that correlates significantly with both aerosol optical depth and cloud fraction is the 10‐meter wind speed. Constructing the partial correlation between aerosol optical depth and cloud fraction, with the impact from 10‐meter wind speed removed, yields a significant difference compared to the total correlation. In several regions the remaining partial correlation is reduced from 0.4 to below 0.1. The results highlight the need to investigate all possible correlations between meteorological variables, cloud properties and aerosols.
Global‐scale black carbon profiles observed in the remote atmosphere and compared to models
Authors: Schwarz J. P. , Spackman J. R. , Gao R. S. , Watts L. A. , Stier P. , Schulz M. , Davis S. M. , Wofsy S. C. , Fahey D. W.
Published: September 2010

Refractory black carbon (rBC) aerosol loadings and mass size distributions have been quantified during the HIPPO campaign above the remote Pacific from 80N to 67S. Over 100 vertical profiles of rBC loadings, extending from ∼0.3 to ∼14 km were obtained with a Single‐Particle Soot Photometer (SP2) during a two‐week period in January 2009. The dataset provides a striking, and previously unobtainable, pole‐to‐pole snapshot of rBC mass loadings. rBC vertical concentration profiles reveal significant dependences on latitude, while associated rBC mass size distributions were highly uniform. The vertical profiles averaged in five latitude zones were compared to an ensemble of AEROCOM model fields. The model ensemble spread in each zone was over an order of magnitude, while the model average over‐predicted rBC concentrations overall by a factor five. The comparisons suggest that rBC removal in global models may need to be evaluated separately in different latitude regions and perhaps enhanced.
Monitoring very‐long‐period seismicity at Kilauea Volcano, Hawaii
Authors: Dawson Phillip B. , Benítez M. C. , Chouet Bernard A. , Wilson David , Okubo Paul G.
Published: September 2010

On 19 March, 2008 eruptive activity returned to the summit of Kilauea Volcano, Hawaii with the formation of a new vent within the Halemaumau pit crater. The new vent has been gradually increasing in size, and exhibiting sustained degassing and the episodic bursting of gas slugs at the surface of a lava pond ∼200 m below the floor of Halemaumau. The spectral characteristics, source location obtained by radial semblance, and Hidden Markov Model pattern recognition of the degassing burst signals are consistent with an increase in gas content in the magma transport system beginning in October, 2007. This increase plateaus between March – September 2008, and exhibits a fluctuating pattern until 31 January, 2010, suggesting that the release of gas is slowly diminishing over time.
Climatology of globally averaged thermospheric mass density
Authors: Emmert J. T. , Picone J. M.
Published: September 2010

We present a climatological analysis of daily globally averaged density data, derived from orbit data and covering the years 1967–2007, along with an empirical Global Average Mass Density Model (GAMDM) that encapsulates the 1986–2007 data. The model represents density as a function of the F10.7 solar radio flux index, the day of year, and the Kp geomagnetic activity index. We discuss in detail the dependence of the data on each of the input variables, and demonstrate that all of the terms in the model represent consistent variations in both the 1986–2007 data (on which the model is based) and the independent 1967–1985 data. We also analyze the uncertainty in the results, and quantify how the variance in the data is apportioned among the model terms. We investigate the annual and semiannual variations of the data and quantify the amplitude, height dependence, solar cycle dependence, and interannual variability of these oscillatory modes. The auxiliary material includes Fortran 90 code for evaluating GAMDM.
Substorm cycle dependence of various types of aurora
Authors: Newell Patrick T. , Lee Anna R. , Liou Kan , Ohtani Shin‐I. , Sotirelis Thomas , Wing Simon
Published: September 2010

We combine 4861 identifications of substorm onsets from satellite global imagers (Polar UVI and IMAGE FUV) with DMSP particle data to investigate the substorm cycle dependence of the diffuse aurora (electrons and ions), monoenergetic aurora (produced by quasi‐static electric fields), and broadband aurora (associated with Alfvénic acceleration). Although all types of aurora increase at substorm onset, broadband aurora shows a particular association with substorms and, especially, substorm onset. While diffuse electron and monoenergetic auroral precipitating power rises by 79% and 90%, respectively, following an onset, wave aurora rises by 182%. In the first 10–15 min following onset, the power associated with Alfvénic acceleration is comparable to monoenergetic acceleration (also called “inverted V” events). In general, this is not the case before onset, or indeed, during recovery. The rise time of the electron diffuse aurora following onset is much slower, about 50 min, and thus presumably extends into recovery. Discrete acceleration, which rises over just a few minutes, is already deep into decline, while diffuse auroral power is still rising. Most of the sharp increase in Alfvénic precipitating power at onset is associated with a 132% jump in the characteristic energy associated with broadband acceleration. Previous work has associated PiB signatures (which are compressional) in the magnetotail with dipolarization. More recently, FAST observations near the auroral zone have been used to show that there are nearly simultaneous sharp increases in Alfvén waves, apparently created by mode coupling. The present work strongly supports the idea that the Alfvénic aurora has a particular connection to substorm onsets, with much of the auroral power over a substorm cycle concentrated shortly after onset. Finally, a superposed epoch analysis of commonly used coupling functions indicates a drop in the mean solar wind driving starting 20 min before substorm onset. However, the distribution of increases and decreases in solar wind driving is roughly symmetric about a peak at zero (no change) but with (rare) large drops in solar wind driving (“northward turnings”) outweighing large increases. Comparison with the distribution of random changes in solar wind driving leads us to suggest that probably only a minority of substorms are externally driven.
Enhancement and HF Doppler observations of sporadic‐E during the solar eclipse of 22 July 2009
Authors: Chen Gang , Zhao Zhengyu , Yang Guobin , Zhou Chen , Yao Ming , Li Ting , Huang Shou , Li Ning
Published: September 2010

The sporadic E (Es) frequently emerging in midlatitude during summer is a very special layer in the ionosphere, and its formation mechanism is different to from that of other layers. The total solar eclipse of 22 July 2009 provided a very unique opportunity to study the relationship of Es and solar radiation. During the solar eclipse day and the days before and after, the vertical incidence ionosonde was located in Wuhan to record the ionograms for this event. Two oblique incidence high‐frequency radio systems were used to record the waves from Wuhan to Suzhou and from Wuhan to Huaian. The enhancement of Es during the eclipse period was observed in the vertical and oblique incidence ionograms. The quasi‐periodic fluctuations in the critical frequency and Doppler frequency shift curves indicated the possible existence of the gravity waves, which may be responsible for the Es enhancement. However, we find that the enhancement occurred earlier than the appearance of gravity waves and consider that there may be other mechanisms which contribute to the observed enhancement in the ionosphere. A hypothesis is put forward that the cooling effect of the lunar shadow induced powerful airflow from the northern and southern limits of the shadow toward its center, which accelerated the irregularities in Es to produce the large‐scale Doppler shift in the reflected waves and form the meridional windshear. Both the windshear and the gravity waves may affect the Es layer and increase the electron concentration. Many observed phenomena are in accordance with this.
Sulfate sources and oxidation chemistry over the past 230 years from sulfur and oxygen isotopes of sulfate in a West Antarctic ice core
Authors: Kunasek S. A. , Alexander B. , Steig E. J. , Sofen E. D. , Jackson T. L. , Thiemens M. H. , McConnell J. R. , Gleason D. J. , Amos H. M.
Published: September 2010

The sulfur and oxygen isotopic composition of sulfate in polar ice cores provides information about atmospheric sulfate sources and formation pathways, which have been impacted regionally by human activity over the past several centuries. We present decadal scale mean ice core measurements of Δ17O, δ34S, Δ33S, and Δ36S of sulfate over the past 230 years from the West Antarctic Ice Sheet (WAIS) Divide deep ice core drill site (WDC05‐A). The low mean δ34S of non–sea‐salt sulfate at WAIS Divide (6.0 ± 0.2‰) relative to East Antarctic coastal and plateau sites may reflect a combination of stronger influence of volcanogenic and/or stratospheric sulfate with low δ34S and the influence of frost flowers on the sea‐salt sulfate‐to‐sodium ratio. Δ33S and Δ36S measurements are all within analytical uncertainty of zero but do not contradict a contribution of stratospheric sources to background sulfate deposition at WAIS Divide. Δ17O of non–sea‐salt sulfate shows a small but significant increase between the late 1700s (1.8‰ ± 0.2‰) and late 1800s (2.6‰ ± 0.2‰), but the influence of stratospheric scale volcanic events on Δ17O in the early 1800s remains uncertain. An isotope mass balance model shows that the lack of change in Δ17O of non–sea‐salt sulfate from the mid‐1800s to early 2000s (2.4‰–2.6‰ ± 0.2‰) is consistent with previous atmospheric chemistry model estimates indicating preindustrial to industrial increases in O3 as high as 50% and decreases in OH of 20% in the southern polar troposphere, as long as H2O2 concentrations also increase by over 50%.
An estimate of aerosol indirect effect from satellite measurements with concurrent meteorological analysis
Authors: Su Wenying , Loeb Norman G. , Xu Kuan‐Man , Schuster Gregory L. , Eitzen Zachary A.
Published: September 2010

Many studies have used satellite retrievals to investigate the effect of aerosols on cloud properties, but these retrievals are subject to artifacts that can confound interpretation. Additionally, large‐scale meteorological differences over a study region dominate cloud dynamics and must be accounted for when studying aerosol and cloud interactions. We have developed an analysis method which minimizes the effect of retrieval artifacts and large‐scale meteorology on the assessment of the aerosol indirect effect. The method divides an oceanic study region into 1° × 1° grid boxes and separates the grid boxes into two populations according to back trajectory analysis: one population contains aerosols of oceanic origin, and the other population contains aerosols of continental origin. We account for variability in the large‐scale dynamical and thermodynamical conditions by stratifying these two populations according to vertical velocity (at 700 hPa) and estimated inversion strength and analyze differences in the aerosol optical depths, cloud properties, and top of atmosphere (TOA) albedos. We also stratify the differences by cloud liquid water path (LWP) in order to quantify the first aerosol indirect effect. We apply our method to a study region off the west coast of Africa and only consider single‐layer low‐level clouds. We find that grid boxes associated with aerosols of continental origin have higher cloud fraction than those associated with oceanic origin. Additionally, we limit our analysis to those grid boxes with cloud fractions larger than 80% to ensure that the two populations have similar retrieval biases. This is important for eliminating the retrieval biases in our difference analysis. We find a significant reduction in cloud droplet effective radius associated with continental aerosols relative to that associated with oceanic aerosols under all LWP ranges; the overall reduction is about 1.0 μm, when cloud fraction is not constrained, and is about 0.5 μm, when cloud fraction is constrained to be larger than 80%. We also find significant increases in cloud optical depth and TOA albedo associated with continental aerosols relative to those associated with oceanic aerosols under all LWP ranges. The overall increase in cloud optical depth is about 0.6, and the overall increase in TOA albedo is about 0.021, when we do not constrained cloud fraction. The overall increases in cloud optical depth and TOA albedo are 0.4 and 0.008, when we only use grid boxes with cloud fraction larger than 80%.
Assimilation of Kalpana very high resolution radiometer water vapor channel radiances into a mesoscale model
Authors: Singh Randhir , Pal P. K. , Joshi P. C.
Published: September 2010

The very high resolution radiometer (VHRR) channel 3 (at 6.2 μm) on the Indian Geostationary satellite Kalpana is sensitive to mid‐upper tropospheric water vapor. This paper describes the assimilation of Kalpana VHRR channel 3 clear‐sky radiances (hereafter water vapor (WV) radiances) in the Weather Research and Forecasting (WRF) three‐dimensional variational assimilation (3D‐Var) system. The Kalpana WV radiances (in terms of blackbody equivalent brightness temperatures) are used in combination with a fast radiative transfer model and 3D‐Var assimilation system in the WRF model. Extensive preassimilation monitoring of the WV radiances has been carried out, showing a diurnal bias of approximately 1 K in the Kalpana WV radiances compared to radiances simulated from the WRF model first‐guess fields. The control (without Kalpana WV radiances) as well as experimental (which assimilated bias corrected Kalpana WV radiances) runs were made for 24 h starting at 0000 UTC during July 2008. The assimilation experiments for July 2008 (22 cases) demonstrated a positive impact of the assimilated Kalpana WV radiances on both the analysis state as well as subsequently short‐term (6–24 h) forecasts. At 0 h (analysis), the agreement of mid‐upper tropospheric moisture sensitive channels (channels 11 and 12) in NOAA/HIRS, which is an independent observation, is improved (improvement is 19% for channel 11 and 17% for channel 12) with the assimilation of Kalpana WV radiances compared to control experiment. In the radiance assimilation experiment, at 6 h (24 h), the root mean square differences between model equivalent Kalpana WV radiances and Kalpana observed WV radiances showed an improvement of 20% (1.7%) relative to the control experiment. Compared with National Center for Environmental Prediction analysis, assimilation of Kalpana WV radiances shows positive impact on the mid‐upper tropospheric moisture and a neutral impact on the temperature and wind forecasts. Compared with atmospheric infrared sounder retrieved and radiosonde observed thermodynamic profiles, Kalpana radiances show positive impact on the mid‐upper tropospheric moisture and temperature and a mixed (negative/positive) impact on the lower and upper tropospheric moisture and temperature forecasts. The comparison of model predicted rainfall with TRMM measurements indicates that Kalpana radiances impacted the rainfall positively.
Observations of near‐surface carbon monoxide from space using MOPITT multispectral retrievals
Authors: Worden H. M. , Deeter M. N. , Edwards D. P. , Gille J. C. , Drummond J. R. , Nédélec P.
Published: September 2010

Using both thermal infrared (TIR) and near infrared (NIR) channels of MOPITT (Measurements of Pollution in the Troposphere) on EOS‐Terra, we demonstrate the first coincident multispectral retrievals of carbon monoxide (CO) from space. Exploiting both TIR and NIR channels has been possible due to recent progress in characterizing NIR channel radiance errors. This has allowed us to trade off sensitivity to near surface CO for larger random errors in the combined retrieval. By examining retrieval diagnostics such as DFS (degrees of freedom for signal) and averaging kernels for the multispectral retrieval (TIR + NIR) as compared to the TIR‐only retrieval, we find that adding the NIR channel to the retrieval significantly increases sensitivity to CO, especially near the surface, but with high spatial variability due to surface albedo variations. The cases with the largest increases in DFS are over regions with low thermal contrast between the surface and lower atmosphere. In the tropics (23.4°S–23.4°N), the fraction of daytime land cases with at least 0.4 DFS in the surface layer (surface to 800 hPa) is 20% for TIR‐only retrievals compared to 59% for multispectral retrievals. Vertical resolution for the surface layer is also improved, in some cases from around 6 km for TIR‐only to roughly 1 km for TIR + NIR. Since we apply a single a priori CO profile (unlike MOPITT V4) and error covariance in all the retrievals reported here, these increases are due solely to the addition of the NIR channel. Enhanced sensitivity to near surface CO is especially evident in a case study for central/east Asia where source regions for urban areas with high population density are clearly identifiable. Although these retrievals are still a research product and require further validation and scientific evaluation, they demonstrate the increased sensitivity to CO in the lowermost troposphere that can be obtained from multispectral MOPITT data.
Growth rates during coastal and marine new particle formation in western Ireland
Authors: Ehn Mikael , Vuollekoski Henri , Petäjä Tuukka , Kerminen Veli‐Matti , Vana Marko , Aalto Pasi , de Leeuw Gerrit , Ceburnis Darius , Dupuy Regis , O'Dowd Colin D. , Kulmala Markku
Published: September 2010

Growth rates of new particles during coastal and marine secondary aerosol particle formation events were studied in western Ireland, both at the Mace Head atmospheric research station and onboard the R/V Celtic Explorer as part of the Marine Aerosol Production project. Strong new particle formation events are frequently detected at Mace Head caused by the emission of precursor gases from exposed seaweed during low tide. Although these events were usually only detected as a mode of particles at a certain size, we were able to link the size of the mode to the growth time of these particles after the initial formation by combining data from several events measured between January 2006 and November 2007 with an air ion spectrometer. Typically, the early growth rates were extremely high, reaching values of several hundred nanometers per hour during the first seconds. The growth rates rapidly decreased and reached values below 1 nm h−1 within 1 h after nucleation. Our results were reproduced with box model calculations. All the obtained growth rates could be explained by the model either by varying the precursor formation time (typically a few seconds) or allowing multiple precursor vapor additions. From the ship‐borne measurements, we report the first observations of purely open ocean new particle formation detected in this region. In total, four events were detected during this period, with three having a variable continental influence. An estimated average growth rate in marine conditions was 3 nm h−1 for these events.
Diversity of Helicobacter pylori among Chinese persons with H. pylori infection
Authors: Yakoob JAVED , Hu GUO LING , Fan XUE GONG , Yang HUI XIANG , Liu SHUANG HU , Tan DE MING , Li TIE GAN , Zhang ZHENG
Published: September 2010

To determine whether there is diversity among clinical isolates of Helicobacter pylori in Chinese patients with peptic ulcer disease, 40 strains of H. pylori were isolated from antral biopsy specimens obtained at the gastroenterology clinic of Xiangya Hospital from January 1996 to June 1998. Total protein profile by sodium dodecyl sulphate‐polyacrylamide gel electrophoresis (SDS‐PAGE) and DNA diversity by polymerase chain reaction‐random amplified polymorphic DNA (PCR‐RAPD) fingerprinting were performed with these isolates. All the isolates from peptic ulcer disease were relatively homogeneous in protein profiles, but they showed a great DNA sequence diversity by PCR‐RAPD fingerprinting. In Chinese patients H. pylori demonstrated an enormous diversity. The diversity among clinical isolates of H. pylori could be distinctly demonstrated and this observation will be helpful in the management of intrafamilial and recurrent H. pylori infection. PCR‐RAPD fingerprinting is an efficient method of distinguishing between clinical isolates of H. pylori.
Oral administration of a nitric oxide synthase inhibitor enhances de novo mammalian angiogenesis mediated by TNF‐alpha, saline and mast‐cell secretion
Authors: Norrby KLAS
Published: September 2010

In healthy adult rats, the test tissue that is used in the mesenteric‐window angiogenesis assay is natively vascularized, lacks physiological angiogenesis, and is unperturbed by surgical intervention. Using the rat MWAA oral treatment with the nitric oxide (NO) synthase inhibitor Nw‐nitro‐L‐arginine methyl ester (L‐NAME) enhanced the angiogenic response (compared with controls receiving the inactive enantiomer D‐NAME) following i.p. injections of (i) TNF‐alpha at an approximate physiological dose, (ii) Compound 48/80, which is a highly selective secretagogue causing mast‐cell secretion in situ and a very strong angiogenic response, and (iii) saline of a grade not made for infusion, causing a weak angiogenic response. Angiogenesis was assessed quantitatively using microscopic morphometry and image analysis in terms of objective variables recording the microvascular spatial extension, microvascular density, number and length of microvessel segments (extending between two successive branching points) and the degree of microvessel tortuosity. The data strongly suggest that endogenous NO inhibits all three mammalian angiogenesis reactions, although to a markedly different extent. Notably, the present data are virtually the opposite of those that have been reported from other mammalian angiogenesis models, the test tissues of which display deranged homeostasis, such as surgical intervention and/or ischemia.
Development of high‐grade lymphoma in Helicobacter pylori‐infected C57BL/6 mice
Authors: Wang XIN , WillÉN ROGER , Andersson CHRISTINA , WadstrÖM TORKEL
Published: September 2010

Helicobacter pylori infection is associated with chronic gastritis, peptic ulcer disease, gastric adenocarcinoma and MALT lymphoma. Mice with H. pylori infection develop severe gastritis and atrophic changes in their stomachs after 6 months. We followed H. pylori‐infected animals for 13 months to find out whether dysplasia, carcinoma or lymphoma developed. Six‐week‐old C57BL/6 mice were infected with the CagA‐positive and VacA‐positive H. pylori mouse‐passaged strain 119/95, fed a low antioxidant diet, and kept in microisolated cages. Histopathological changes were examined after 13 months' infection. All H. pylori‐inoculated mice (n=5) developed a gastric squamous papilloma with nagging of the lamina muscularis after 13 months. Three out of five animals developed high‐grade B‐cell lymphoma derived from a MALT lymphoma at the squamous‐corpus border with manifestations also in the liver, spleen and kidney. There was a suspicion of local gastric lymphoma in the two remaining mice but with no significant changes in the liver, spleen or kidney. The normal control mice showed no pathological changes in any of these organs. It is concluded that this mouse model with infection by the CagA‐positive, vac‐toxin‐producing H. pylori strain 119/95 is suitable for use in the study of lymphoma development and also development of squamous cell papilloma with proliferative features.
Genosubtyping by sequencing group A, B and C meningococci; a tool for epidemiological studies of epidemics, clusters and sporadic cases
Authors: MÖLling PAULA , Unemo MAGNUS , Backman ANDERS , OlcÉN PER
Published: September 2010

Genosubtyping, by sequencing variable regions (VRs) 1, 2 and 3 of the porA gene, was evaluated as a tool to detect clonality of isolates in meningococcal epidemics in Africa and clusters of disease in Sweden. All 63 examined meningococcal isolates were successfully genosubtyped. The isolates belonging to group A type 4 with genosubtype P1.20,9,35a showed little heterogeneity in African epidemics in 1988 and onwards. In Sweden, two meningococcal clones of group B type 15, with genosubtypes P1.7,16,35 and P1.7,16f,35, dominated during two clusters of meningococcal disease in 1995–96 and in sporadic cases thereafter. The characterisation of group C meningococci isolated during 1992 in Sweden indicated a cluster (type 2a with genosubtype P1.5a,10d,36b) connected with a discotheque visit. Two variants of VR2 (10p and 25b), not previously described, were found among the examined isolates. Nucleotide sequence analysis of VRs in the porA gene proved a valuable epidemiological tool since almost all isolates could be genosubtyped, in contrast to the phenotypic methods presently used.
Evaluation of calibrated 1 and 10 μl loops and dipslide as compared to pipettes for detection of low count bacteriuria in vitro
Authors: Frimodt‐MØLler NIELS , Espersen FRANK
Published: September 2010

Criteria for defining urinary tract infection have changed as the importance of low count bacteriuria in patients with symptoms of infection has been recognized. Little has been published, however, regarding the ability of routine laboratory methods to meet this new challenge. We compared 1 μl and 10 μl calibrated plastic loops (Nunc, Denmark), to a commonly used dipslide method (Uricult, Orion, Finland) using a 0.1 ml pipette as the gold standard. Four typical uropathogens, E. coli, P. aeruginosa, S. saprophyticus and E. faecalis, were mixed in pooled human urine in numbers representing low counts, i.e. 102, 103, and 104, together with 105colony‐forming units (cfu)/ml, and sampling with the four methods was performed 20 times for each with each bacterium and each dilution. Colony counts showed that in many cases the 1 μl loop did not deposit any bacteria on the agar plate when colony counts were lower than 104cfu/ml. The 10 μl loop constantly deposited 1.5 times higher numbers of bacteria than predicted, which correlated with the results of weighing the amount of water sampled, i.e. 15.24 (1.55) μg (mean (SD)). The dipslide counts correlated with the 10 μl loop although the agar mounts on the slides absorbed water equal to about 200 μl. There were no significant differences in the counts of the four different bacteria. Variation coefficients increased with decreasing volumes sampled, but the 10 μl loop was found sufficiently exact to detect counts from 103to 104, since only 10‐fold multiples are usually reported for urine cultures.
The emerging phenotype of the testicular carcinoma in situ germ cell
Authors: RAJPERT‐DE MEYTS EWA , BARTKOVA JIRINA , SAMSON MICHEL , HOEI‐HANSEN CHRISTINA E. , FRYDELUND‐LARSEN LONE , BARTEK JIRI , SKAKKEBæK NIELS E.
Published: September 2010

This review summarises the existing knowledge on the phenotype of the carcinoma in situ (CIS) cell. CIS is a common pre‐invasive precursor of testicular germ cell tumours of adolescents and young adults. These tumours display a variety of histological forms. Classical seminoma proliferates along the germ cell lineage, whereas embryonal carcinoma retains embryonic features and readily differentiates into teratomas that resemble various somatic cell lineages. A thorough review of the gene expression in CIS cells in comparison to normal testicular germ cells and overt tumours supports the view that CIS is a common precursor for both tumour types. Impaired cell differentiation resulting in a partial retention of the embryonic features, associated with an increasing genomic instability may be responsible for a remarkable phenotypic heterogeneity of CIS cells. Depending on the degree of differentiation and pluripotency, CIS cells found in adult patients seem to be predestined for further malignant progression into one or the other of the two main types of overt tumours. A new concept of phenotypic continuity of differentiation of germ cells along germinal lineage with a gradual loss of embryonic features based on the analysis of gene expression in all types of germ cells during their ontogeny is presented in this review. The data point out that despite the phenotypic continuum of gene expression, there are two periods of rapid changes of gene expression: first at the transition from primordial germ cells to pre‐spermatogonia, and later during the pubertal switch from the mitotic to meiotic cell division. The persistent expression of embryonic traits in CIS cells, and the high expression of the cell cycle regulators that are typical of mitotic germ cells support our long‐standing hypothesis that CIS cells originate from primordial germ cells or gonocytes and not from germ cells in the adult testis.
Comparison of the chromatographic properties of IgG1 and IgG2 antibody subclasses
Authors: Ghose Sanchayita , Ladwig Justin , Allen Martin
Published: September 2010

All therapeutic antibodies that are currently approved or under development are IgGs, with IgG1 and IgG2 being the most prevalent subclasses. The present study investigates the effect of antibody subclass on its chromatographic properties. To this end, two sets of antibodies with identical variable domains and differing subclasses (IgG1 and IgG2) were compared by using purification methods that are most commonly used in industrial antibody manufacturing processes. Each antibody was examined using Protein A chromatography, cation‐exchange chromatography, hydrophobic interaction chromatography and salt‐induced precipitation studies. The results of these experiments show that the variable region of an antibody has a greater influence on its chromatographic behaviour than antibody subclass.
Translocation of the Na+/H+ exchanger 1 (NHE1) in cardiomyocyte responses to insulin and energy-status signalling
Authors: Lawrence Scott P. , Holman Geoffrey D. , Koumanov Françoise
Published: September 2010

The Na+/H+ exchanger NHE1 is a highly regulated membrane protein that is required for pH homoeostasis in cardiomyocytes. The activation of NHE1 leads to proton extrusion, which is essential for counteracting cellular acidity that occurs following increased metabolic activity or ischaemia. The activation of NHE1 intrinsic catalytic activity has been well characterized and established experimentally. However, we have examined in the present study whether a net translocation of NHE1 to the sarcolemma of cardiomyocytes may also be involved in the activation process. We have determined the distribution of NHE1 by means of immunofluorescence microscopy and cell-surface biotinylation. We have discovered changes in the distribution of NHE1 that occur when cardiomyocytes are stimulated with insulin that are PI3K (phosphoinositide 3-kinase)-dependent. Translocation of NHE1 also occurs when cardiomyocytes are challenged by hypoxia, or inhibition of mitochondrial oxidative metabolism or electrically induced contraction, but these responses occur through a PI3K-independent process. As the proposed additional level of control of NHE1 through translocation was unexpected, we have compared this process with the well-established translocation of the glucose transporter GLUT4. In immunofluorescence microscopy comparisons, the translocation of NHE1 and GLUT4 to the sarcolemma that occur in response to insulin appear to be very similar. However, in basal unstimulated cells the two proteins are mainly located, with the exception of some co-localization in the perinuclear region, in distinct subcellular compartments. We propose that the mechanisms of translocation of NHE1 and GLUT4 are linked such that they provide spatially and temporally co-ordinated responses to cardiac challenges that necessitate re-adjustments in glucose transport, glucose metabolism and cell pH.
Functional complexes between YAP2 and ZO-2 are PDZ domain-dependent, and regulate YAP2 nuclear localization and signalling
Authors: Oka Tsutomu , Remue Eline , Meerschaert Kris , Vanloo Berlinda , Boucherie Ciska , Gfeller David , Bader Gary D. , Sidhu Sachdev S. , Vandekerckhove Joël , Gettemans Jan , Sudol Marius
Published: September 2010

The Hippo pathway regulates the size of organs by controlling two opposing processes: proliferation and apoptosis. YAP2 (Yes kinase-associated protein 2), one of the three isoforms of YAP, is a WW domain-containing transcriptional co-activator that acts as the effector of the Hippo pathway in mammalian cells. In addition to WW domains, YAP2 has a PDZ-binding motif at its C-terminus. We reported previously that this motif was necessary for YAP2 localization in the nucleus and for promoting cell detachment and apoptosis. In the present study, we show that the tight junction protein ZO (zonula occludens)-2 uses its first PDZ domain to form a complex with YAP2. The endogenous ZO-2 and YAP2 proteins co-localize in the nucleus. We also found that ZO-2 facilitates the nuclear localization and pro-apoptotic function of YAP2, and that this activity of ZO-2 is PDZ-domain-dependent. The present paper is the first report on a PDZ-based nuclear translocation mechanism. Moreover, since the Hippo pathway acts as a tumour suppressor pathway, the YAP2–ZO-2 complex could represent a target for cancer therapy.
Comparison of the substrate kinetics of pig CYP3A29 with pig liver microsomes and human CYP3A4
Authors: Yao Min , Dai Menghong , Liu Zhaoying , Huang Lingli , Chen Dongmei , Wang Yulian , Peng Dapeng , Wang Xu , Liu Zhenli , Yuan Zonghui
Published: September 2010

CYP (cytochrome P450) 3A29 in pigs could be an important candidate gene responsible for xenobiotic metabolism, similar to CYP3A4 in humans. Accordingly, the tissue expression of CYP3A29 mRNA in domestic pigs has been determined by a real-time PCR. The enzymatic properties of CYP3A29, CYP3A4 and PLM (pig liver microsomes) were compared by kinetic analysis of TST (testosterone) 6β-hydroxylation and NIF (nifedipine) oxidation. CYP3A29 mRNA was highly expressed in the liver and small intestines of domestic pigs. The CYP3A29 enzyme expressed in Sf9 cells had the same TST-metabolizing activity as human CYP3A4 based on their roughly equal in vitro intrinsic clearance values. The affinity of CYP3A29 for NIF was lower than that of CYP3A4 but higher than that of PLM. KET (ketoconazole) was a more potent inhibitor of TST 6β-hydroxylation and NIF oxidation activities of CYP3A29 than TAO (troleandomycin). These findings indicate that pig CYP3A29 is similar to human CYP3A4 in both extent of expression and activity. The results reported in this paper provide a basis for future in vitro toxicity and metabolism studies.
Hemolytic transfusion reaction due to anti‐A
Authors: Lundberg W. B. , McGinnis M. H.
Published: September 2010

A hemolytic transfusion reaction in an A2B patient due to anti‐A1 is described. Anti‐A1 was first detected simultaneously with the removal of transfused A1 red blood cells. The antibody in the serum was shown to be of both the IgM and IgG class, but only IgG was demonstrated on and eluted from sensitized, transfused red blood cells. 51Cr survival studies of A1 red blood cells demonstrated the hemolytic capability of this antibody on two occasions.
Transfusion Reactions Associated with Anti‐IgA Antibodies: Report of Four Cases and Review of the Literature
Authors: Pineda A. A. , Taswell H. F.
Published: September 2010

Four cases of anaphylactic and anaphylactoid transfusion reactions associated with anti‐IgA antibodies are reported. Two were class‐specific and two were of limited specificity. All four patients had serious reactions characterized by hypotension, dyspnea, flushing of face and neck, or erythematous rash after administration of otherwise compatible blood. In one patient this reaction was fatal. In another, diagnosis of the condition based on previous transfusion history prevented a subsequent reaction. Review of the literature reveals an apparently low incidence of reactions but a relatively large susceptible population with anti‐IgA. Reported reactions have occurred equally in both sexes and largely in patients over 40 years of age who previously have been transfused or pregnant. Although severe and dramatic, these reactions have responded well to treatment and generally have not had serious sequelae.
An Anti‐Neomycin Antibody Interfering with ABO Grouping and Antibody Screening
Authors: Hysell J. K. , Gray J. M. , Hysell J. W. , Keck M. L.
Published: September 2010

A patient's serum agglutinated most commercial antibody screening and panel identification red blood cells; however, it did not agglutinate either the cells of ABO compatible donors or washed, saline suspended commercial cells. When suspended in a solution containing 0.1 mg/ml neomycin, all cells, including the patient's, were agglutinated by the patient's serum.

Inhibition did not occur by preincubation of either the patient's serum or the test cells with 10 mg/ml neomycin. Serum preincubation with butirosin, kanamycin, or neamine inhibited immediate agglutination in the presence of neomycin. The reactive group is, therefore, included in the neamine fragment.

Ultracentrifugation segregated the antibody in the 7S fraction. Following separation by column chromatography, only fractions containing IgA demonstrated antineomycin activity.
The Use of Dextran as an Adjunct to Granulocyte Collection with the Continuous‐Flow Blood Cell Separator
Authors: Lowenthal R. M. , Park D. S.
Published: September 2010

High molecular weight dextran (dextran 110 or 150 in saline) was added to the input line of the continuous‐flow blood cell separator during a series of procedures for the collection of granulocytes from normal donors. Compared with procedures in which dextran was not used, there was enhanced sedimentation of red blood cells within the centrifuge bowl, and analysis of serial samples taken from the white blood cell line showed that contamination of the buffy coat by red cells was reduced by 88 per cent at the point where the granulocyte count was highest. The total leukocyte yields were 1.0 × 1010 cells when dextran was not used (five procedures), 1.6 × 1010 cells with dextran 110 (28 procedures), and 2.3 × 1010 cells with dextran 150 (20 procedures), and there were corresponding increases in the numbers of granulocytes collected. The technique has proved safe and simple, and the addition of dextran is recommended as a means of increasing the leukocyte yield from normal donors while reducing the number of red blood cells collected.
A Comparison of Platelet Production Methods Suitable for a Service‐Oriented Blood Donor Center
Authors: Koepke J. A. , Wu K. K. , Hoak J. C. , Thompson J. S.
Published: September 2010

A comparison of two methods of producing platelets for transfusion reveals similar efficiencies between the standard double plateletpheresis method and the Latham Blood Processor. The platelets produced are similar in size and survival. The double plateletpheresis system is somewhat cheaper especially in lower volume production systems and allows for the simultaneous production of cryoprecipitate and other plasma products. The Latham system, on the other hand, has the advantage of production of larger number of platelets obtained from individual donors.
A Kininogen‐Like Substance in Unheated Human Plasma Proteins
Authors: Izaka K. , Morichi S. , Fujita Y. , Hasegawa E.
Published: September 2010

The presence of a kininogen‐like substance was evidenced in unheated human plasma proteins. This substance was found to be susceptible to human urinary kallikrein and its content per gram dry weight of unheated plasma proteins was estimated to be equal to the amount of standard human kininogen that produces kinin activity equivalent to 2–8 μg bradykinin under the action of human urinary kallikrein.

The elimination of this substance from unheated plasma proteins was achieved by chromatography on DEAE‐Sephadex equilibrated with pH 7.5 Tris buffer. The bradykinin‐like substance contained in 5 per cent heat‐treated human plasma protein solution was demonstrated to be released either by the heat treatment of unheated plasma protein solution at 60 C or by the enzymatic action of human urinary kallikrein. It is presumed that this kininogen‐like substance in unheated plasma proteins will be a precursor for the bradykinin‐like substance in 5 per cent heat‐treated human plasma protein solution.
Mixed‐Field Polyagglutinability Due to Tn: A Further Example
Authors: Moore B. P. L. , Marsh S. , Laschinger C. , Simpson S.
Published: September 2010

Mixed‐field polyagglutination of red blood cells caused by the presence of the determinant Tn can be distinguished from other causes of polyagglutination such as T and Cad [Sd(a ++)] by tests with four plant hemagglutinins—Doliches biflorus, Arachis hypogaea, Salvia sclarea, and Salvia horminum. Inhibition of the reactions of Tn cells with Dolichos biflorus and Salvia horminum when the cells are pretreated with papain and negative reactions of Tn cells with sera from other known cases lend support to the diagnosis.
Direct Antiglobulin Tests in Narcotic Addicted Patients
Authors: Cushman P. , Maniatis A.
Published: September 2010

Direct Antiglobulin Tests (DAT) as well as a number of immunological parameters (immunoglobulin levels, latex fixation, VDRL) were studied in 168 narcotic‐addicted patients. Of these, 94 were untreated narcotic addicts (Group I), 61 were methadone maintained patients (Group II), and 13 had completed successful detoxification with methadone and were drug‐free (Group III). Weakly positive DAT were detected in 2.1 per cent of individuals in Group I, 18 per cent in Group II, and 15 per cent in Group III. The reactions were usually transient. A number of other immunological aberrations were also present in individuals of all three groups, but there was no correlation between these parameters and the positive direct antiglobulin reactions.