bluuebunny/crossref_metadata_2025_split huggingface dataset:
Erroneous Relationships among Humidity and Cloud Forcing Variables in Three Global Climate Models
Authors: Bennhold Florian , Sherwood Steven 
Published: February 2008

Abstract
Links are examined between time-averaged cloud radiative properties, particularly the longwave and shortwave components of cloud radiative forcing (CRF), and properties of the long-term averages of atmospheric soundings, in particular upper-tropospheric humidity (UTH), lower-tropospheric precipitable water (PW), and static stability (SS). The joint distributions of moisture measures and the composite or conditional mean CRF for different moisture and stability combinations are computed. This expands on previous studies that have examined cloud properties versus vertical velocity and surface temperature. These computations are done for satellite observations and for three representative coupled climate models from major modeling centers.
Aside from mean biases reported previously, several departures are identified between the modeled and observed joint distributions that are qualitative and significant. Namely, the joint distribution of PW and UTH is very compact in observations but less so in models, cloud forcings are tightly related to PW in the data but to UTH in the models, and strong negative net CRF in marine stratocumulus regions occurs only for high SS and low UTH in the data but violates one or both of these restrictions in each of the models.
All three errors are preliminarily interpreted as symptoms of inadequate dependence of model convective development on ambient humidity above the boundary layer. In any case, the character of the errors suggests utility for model testing and future development. A set of scalar metrics for quantifying some of the problems is presented; these metrics can be easily applied to standard model output.
Finally, an examination of doubled-CO2 simulations suggests that the errors noted here are significantly affecting cloud feedback in at least some models. For example, in one model a strong negative feedback is found from clouds forming in model conditions that never occur in the observations.
Cloud Effects on the Meridional Atmospheric Energy Budget Estimated from Clouds and the Earth’s Radiant Energy System (CERES) Data
Authors: Kato Seiji , Rose Fred G. , Rutan David A. , Charlock Thomas P. 
Published: February 2008

Abstract
The zonal mean atmospheric cloud radiative effect, defined as the difference between the top-of-the-atmosphere (TOA) and surface cloud radiative effects, is estimated from 3 yr of Clouds and the Earth’s Radiant Energy System (CERES) data. The zonal mean shortwave effect is small, though it tends to be positive (warming). This indicates that clouds increase shortwave absorption in the atmosphere, especially in midlatitudes. The zonal mean atmospheric cloud radiative effect is, however, dominated by the longwave effect. The zonal mean longwave effect is positive in the tropics and decreases with latitude to negative values (cooling) in polar regions. The meridional gradient of the cloud effect between midlatitude and polar regions exists even when uncertainties in the cloud effect on the surface enthalpy flux and in the modeled irradiances are taken into account. This indicates that clouds increase the rate of generation of the mean zonal available potential energy. Because the atmospheric cooling effect in polar regions is predominately caused by low-level clouds, which tend to be stationary, it is postulated here that the meridional and vertical gradients of the cloud effect increase the rate of meridional energy transport by the dynamics of the atmosphere from the midlatitudes to the polar region, especially in fall and winter. Clouds then warm the surface in the polar regions except in the Arctic in summer. Clouds, therefore, contribute toward increasing the rate of meridional energy transport from the midlatitudes to the polar regions through the atmosphere.
Robustness of Future Changes in Local Precipitation Extremes
Authors: Kendon Elizabeth J. , Rowell David P. , Jones Richard G. , Buonomo Erasmo 
Published: February 2008

Abstract
Reliable projections of future changes in local precipitation extremes are essential for informing policy decisions regarding mitigation and adaptation to climate change. In this paper, the extent to which the natural variability of the climate affects one’s ability to project the anthropogenically forced component of change in daily precipitation extremes across Europe is examined. A three-member ensemble of the Hadley Centre Regional Climate Model (HadRM3H) is used and a statistical framework is applied to estimate the uncertainty due to the full spectrum of climate variability. In particular, the results and understanding presented here suggest that annual to multidecadal natural variability may contribute significant uncertainty. For this ensemble projection, extreme precipitation changes at the grid-box level are found to be discernible above climate noise over much of northern and central Europe in winter, and parts of northern and southern Europe in summer. The ability to quantify the change to a reasonable level of accuracy is largely limited to regions in northern Europe. In general, where climate noise has a significant component varying on decadal time scales, single 30-yr climate change projections are insufficient to infer changes in the extreme tail of the underlying precipitation distribution. In this context, the need for ensembles of integrations is demonstrated and the relative effectiveness of spatial pooling and averaging for generating robust signals of extreme precipitation change is also explored. The key conclusions are expected to apply more generally to other models and forcing scenarios.
Equilibrium Response of an Atmosphere–Mixed Layer Ocean Model to Different Radiative Forcing Agents: Global and Zonal Mean Response
Authors: Yoshimori Masakazu , Broccoli Anthony J. 
Published: February 2008

Abstract
The equilibrium response to various forcing agents, including CO2, solar irradiance, tropospheric ozone, black carbon, organic carbon, sulfate, and volcanic aerosols, is investigated using an atmospheric general circulation model coupled to a mixed layer ocean model. The experiments are carried out by altering each forcing agent separately. Realistic spatial patterns of forcing constituents are applied but the magnitude of the forcing is adjusted so that each forcing constituent yields approximately the same strength of radiative forcing. It is demonstrated that the global mean temperature response depends on the types of forcing agents and the efficacy with respect to CO2 forcing ranges from 58% to 100%. The smallest efficacy is seen in one of the black carbon experiments and is associated with negative cloud feedback. The sign of the cloud feedback is shown to be sensitive to the vertical distribution of black carbon. The feedback analysis suggests that the small efficacy in tropospheric ozone is due to a large negative lapse rate feedback. Global mean precipitation increases when the earth warms except for the case of black carbon in which precipitation decreases. In all experiments, the global mean convective mass flux decreases when the earth’s surface warms. When the applied radiative forcing resulting from a particular forcing agent is stronger in one hemisphere, anomalous heat exchange between the hemispheres results in conjunction with changes in the Hadley circulation. The magnitude of interhemispheric heat transport is little sensitive to the details of the forcing, but is determined primarily by the interhemispheric contrast in forcing. The change in the Hadley circulation strongly impacts the precipitation changes in low latitudes.
Boreal Summer Intraseasonal Variability in Coupled Seasonal Hindcasts
Authors: Xavier Prince K. , Duvel Jean-Philippe , Doblas-Reyes Francisco J. 
Published: February 2008

Abstract
The intraseasonal variability (ISV) of the Asian summer monsoon represented in seven coupled general circulation models (CGCMs) as part of the Development of a European Multimodel Ensemble System for Seasonal-to-Interannual Prediction (DEMETER) project is analyzed and evaluated against observations. The focus is on the spatial and seasonal variations of ISV of outgoing longwave radiation (OLR). The large-scale organization of convection, the propagation characteristics, and the air–sea coupling related to the monsoon ISV are also evaluated. A multivariate local mode analysis (LMA) reveals that most models produce less organized convection and ISV events of shorter duration than observed. Compared to the real atmosphere, these simulated patterns of perturbations are poorly reproducible from one event to the other. Most models simulate too weak sea surface temperature (SST) perturbations and systematic phase quadrature between OLR, surface winds, and SST—indicative of a slab-ocean-like response of the SST to surface flux perturbations. The relatively coarse vertical resolution of the different ocean GCMs (OGCMs) limits their ability to represent intraseasonal processes, such as diurnal warm layer formation, which are important for realistic simulation of the SST perturbations at intraseasonal time scales. Models with the same atmospheric GCM (AGCM) and different OGCMs tend to have similar biases of the simulated ISV, indicating the dominant role of atmospheric models in fixing the nature of the intraseasonal variability. It is, therefore, implied that improvements in the representation of ISV in coupled models have to fundamentally arise from fixing problems in the large-scale organization of convection in AGCMs.
Pacific Subtropical Cell Response to Reduced Equatorial Dissipation
Authors: Harrison M. J. , Hallberg R. W. 
Published: February 2008

Abstract
Equatorial turbulent diffusivities resulting from breaking gravity waves may be more than a factor of 10 less than those in the midlatitudes. A coupled general circulation model with a layered isopycnal coordinate ocean is used to assess Pacific climate sensitivity to a latitudinally varying background diapycnal diffusivity with extremely low values near the equator.
The control experiments have a minimum upper-ocean diffusivity of 10−5 m2 s−1 and are initialized from present-day conditions. The average depth of the σθ = 26.4 interface (z26.4) in the Pacific increases by ∼140 m after 500 yr of coupled model integration. This corresponds to a warming trend in the upper ocean. Low equatorial diffusivities reduce the z26.4 bias by ∼30%. Isopycnal surfaces are elevated from the eastern boundary up to midlatitudes by cooling in the upper several hundred meters, partially compensated by freshening. Entrainment of intermediate water masses from below σθ = 26.4 decreases by ∼1.5 Sv (1 Sv ≡ 106 m3 s−1), mainly in the western tropical Pacific. The Pacific heat uptake (30°S–30°N) from the atmosphere reduces by ∼0.1 PW. This is associated with warmer entrainment temperatures in the eastern equatorial Pacific upwelling region. Equatorward heat transport from the Southern Ocean increases by ∼0.07 PW.
Reducing the upper-ocean background diffusivity uniformly to 10−6 m2 s−1 cools the upper ocean from the tropics, but warms and freshens from the midlatitudes. Enhanced convergence into the Pacific of water lighter than σθ = 26.4 compensates the reduction in upwelling of intermediate waters in the tropics. Basin-averaged z26.4 bias increases in the low background case.
These results demonstrate basin-scale sensitivity to the observed suppression of equatorial background dissipation. This has clear implications for understanding oceanic heat uptake in the Pacific as well as other important aspects of the climate system. Diapycnal diffusivities due to truncation errors and other numerical artifacts in ocean models may need to be less than 10−6 m2 s−1 in order to accurately represent this effect in climate models.
A 20-Yr Average of the Indonesian Throughflow: Regional Currents and the Interbasin Exchange
Authors: Wijffels Susan E. , Meyers Gary , Godfrey J. Stuart 
Published: February 2008

Abstract
Twenty years of monthly or more frequent repeat expendable bathythermograph data are used to estimate the mean geostrophic velocity and transport relative to 750 m of the Indonesian Throughflow (ITF) and its partitioning through the major outflow straits into the Indian Ocean. Ekman transports are estimated from satellite and atmospheric reanalysis wind climatologies. A subsurface maximum near 100 m characterizes the geostrophic ITF, but Ekman flows drive a warm near-surface component as well. A subsurface intensified fresh Makassar Jet feeds the Lombok Strait Throughflow (∼2 Sv; 1Sv ≡ 106 m3 s−1) and an eastward flow along the Nusa Tenggara island chain [the Nusa Tenggara Current (6 Sv)]. This flow feeds a relatively cold 3.0-Sv flow through the Ombai Strait and Savu Sea. About 4–5 Sv pass through Timor Passage, fed by both the Nusa Tenggara Current and likely warmer and saltier flow from the eastern Banda Sea. The Ombai and Timor Throughflow feature distinctly different shear profiles; Ombai has deep-reaching shear with a subsurface velocity maximum near 150 m and so is cold (∼15.5°–17.1°C), while Timor Passage has a surface intensified flow and is warm (∼21.6°–23°C). At the western end of Timor Passage the nascent South Equatorial Current is augmented by recirculation from a strong eastward shallow flow south of the passage. South of the western tip of Java are two mean eastward flows—the very shallow, warm, and fresh South Java Current and a cold salty South Java Undercurrent. These, along with the inflow of the Eastern Gyral Current, recirculate to augment the South Equatorial Current, and greatly increase its salinity compared to that at the outflow passages. The best estimate of the 20-yr-average geostrophic plus Ekman transport is 8.9 ± 1.7 Sv with a transport-weighted temperature of 21.2°C and transport-weighted salinity of 34.73 near 110°E. The warm temperatures of the flow can be reconciled with the much cooler estimates based on mooring data in Makassar Strait by accounting for an unmeasured barotropic and deep component, and local surface heat fluxes that warm the ITF by 2°–4°C during its passage through the region.
Ultrasound for Inflammatory Bowel Disease in Gastroenterology; an Introduction to Basic Technique and Image Interpretation
Authors: Dixon Andrew , Rodgers Peter 
Published: February 2008

Bowel ultrasound is often considered as a relatively specialist technique and a lot of sonographers shy away from it, perhaps fearing ridicule from experts in the field. However, as ultrasound becomes more available, and as a wider range of practitioners (like myself) achieve competence, the taboos of specialist ultrasound techniques are being broken down. This paper is a guide to the technique and application of bowel ultrasound for the new or novice practitioner which aims to provide a solid understanding of the technique upon which to build with further experience. Background: Dr Dixon is a medical gastroenterologist (non-radiologist) who has undertaken training and achieved a postgraduate certificate in medical ultrasound. He sees the role of ultrasound for the gastroenterologist, as a direct extension of clinical history taking and a medical examination. With inflammatory bowel disease a common presentation to gastroenterology clinics, he feels that the ability to use ultrasound to scan patients in a safe and reliable way is invaluable. Dr Dixon uses bowel ultrasound as an extended examination and challenges all, with a bit of practice, to embrace the technique and advance their skills. He believes if he can do it… so can everyone else.
Rabbit ATG but not horse ATG promotes expansion of functional CD4+CD25highFOXP3+ regulatory T cells in vitro
Authors: Feng Xingmin , Kajigaya Sachiko , Solomou Elena E. , Keyvanfar Keyvan , Xu Xiuli , Raghavachari Nalini , Munson Peter J. , Herndon Thomas M. , Chen Jichun , Young Neal S. 
Published: February 2008

AbstractRegulatory T cells (Treg) play important roles in suppressing immune responses and maintaining tolerance. Rabbit antithymocyte globulin (rATG) and horse ATG (hATG) are widely used in the treatment of immune-mediated syndromes, but their effects on Treg are unknown. We show here that in vitro culture of normal human peripheral blood mononuclear cells (PBMCs) with a low-dose rATG resulted in marked expansion of functional Treg by converting CD4+CD25− T cells to CD4+CD25+ T cells. hATG did not expand but rather decreased Treg. Immuno-blot showed increased expression of FOXP3 and NFAT1 in CD4+CD25− and CD4+CD25+ T cells exposed to rATG. PBMCs treated with rATG displayed increased interleukin-10 in culture supernatants than those treated with hATG. Furthermore, rATG and hATG showed differences in their potential to stimulate CD4+ T cells as examined using different activation markers. Microarray revealed that rATG induced markedly different gene-expression patterns in PBMCs, compared with hATG-treated or untreated PBMCs. Our findings indicate that rATG expanded Treg, probably through transcriptional regulation by enhanced NFAT1 expression, in turn conferring CD4+CD25− T cell FOXP3 expression and regulatory activity. The therapeutic effects of rATG may occur not only because of lymphocyte depletion but also enhanced Treg cell number and function.
From speciation to introgressive hybridization: the phylogeographic structure of an island subspecies of termite, Reticulitermes lucifugus corsicus
Authors: Lefebvre Thomas , Châline Nicolas , Limousin Denis , Dupont Simon , Bagnères Anne-Geneviève 
Published: February 2008

AbstractBackgroundAlthough much research has been carried out into EuropeanReticulitermestaxonomy in recent years, there is still much discussion about phylogenetic relationships. This study investigated the evolution from intra- to interspecific phylogeny in the island subspeciesReticulitermes lucifugus corsicusand threw new light on this phenomenon. An integrative approach based on microsatellites and mitochondrial and nuclear DNA sequences was used to analyze samples taken from a wide area around the Tyrrhenian sea and showed how the subspecies evolved from its origins to its most recent form on continental coasts.ResultsAccording to mitochondrial phylogeny and molecular clock calculations, island and continental taxa diverged significantly by vicariance in the Pleistocene glacial period. However, more recently, numerous migrations, certainly human-mediated, affected the structure of the populations. This study provided evidence of direct hybridization and multiple introgressions which occurred in several hybrid areas. Analysis using STRUCTURE based on microsatellite data identified a population in Provence (France) which differed considerably (Fst = 0.477) from populations on the island of Corsica and in Tuscany in the Italian peninsula. This new population, principally distributed in urban areas, is highly heterogeneous especially within the ITS2 regions where homogenization by concerted evolution does not appear to have been completed.ConclusionThis study provides an unusual picture of genetic interaction between termite populations in the Tyrrhenian area and suggests that more attention should be paid to the role of introgression and human impact on the recent evolution of European termites.
Prevalence of common disease-associated variants in Asian Indians
Authors: Pemberton Trevor J , Mehta Niyati U , Witonsky David , Di Rienzo Anna , Allayee Hooman , Conti David V , Patel Pragna I 
Published: February 2008

AbstractBackgroundAsian Indians display a high prevalence of diseases linked to changes in diet and environment that have arisen as their lifestyle has become more westernized. Using 1200 genome-wide polymorphisms in 432 individuals from 15 Indian language groups, we have recently shown that: (i) Indians constitute a distinct population-genetic cluster, and (ii) despite the geographic and linguistic diversity of the groups they exhibit a relatively low level of genetic heterogeneity.ResultsWe investigated the prevalence of common polymorphisms that have been associated with diseases, such as atherosclerosis (ALOX5), hypertension (CYP3A5,AGT,GNB3), diabetes (CAPN10,TCF7L2,PTPN22), prostate cancer (DG8S737, rs1447295), Hirschsprung disease (RET), and age-related macular degeneration (CFH,LOC387715). In addition, we examined polymorphisms associated with skin pigmentation (SLC24A5) and with the ability to taste phenylthiocarbamide (TAS2R38). All polymorphisms were studied in a cohort of 576 India-born Asian Indians sampled in the United States. This sample consisted of individuals whose mother tongue is one of 14 of the 22 "official" languages recognized in India as well as individuals whose mother tongue is Parsi, a cultural group that has resided in India for over 1000 years. Analysis of the data revealed that allele frequency differences between the different Indian language groups were small, and interestingly the variant alleles ofALOX5g.8322G>A and g.50778G>A, andPTPN22g.36677C>T were present only in a subset of the Indian language groups. Furthermore, a latitudinal cline was identified both for the allele frequencies of the SNPs associated with hypertension (CYP3A5,AGT,GNB3), as well as for those associated with the ability to taste phenylthiocarbamide (TAS2R38).ConclusionAlthough caution is warranted due to the fact that this US-sampled Indian cohort may not represent a random sample from India, our results will hopefully assist in the design of future studies that investigate the genetic causes of these diseases in India. Our results also support the inclusion of the Indian population in disease-related genetic studies, as it exhibits unique genotype as well as phenotype characteristics that may yield new insights into the underlying causes of common diseases that are not available in other populations.
Analysis of genetic variation in Ashkenazi Jews by high density SNP genotyping
Authors: Olshen Adam B , Gold Bert , Lohmueller Kirk E , Struewing Jeffery P , Satagopan Jaya , Stefanov Stefan A , Eskin Eleazar , Kirchhoff Tomas , Lautenberger James A , Klein Robert J , Friedman Eitan , Norton Larry , Ellis Nathan A , Viale Agnes , Lee Catherine S , Borgen Patrick I , Clark Andrew G , Offit Kenneth , Boyd Jeff 
Published: February 2008

Abstract

Background
Genetic isolates such as the Ashkenazi Jews (AJ) potentially offer advantages in mapping novel loci in whole genome disease association studies. To analyze patterns of genetic variation in AJ, genotypes of 101 healthy individuals were determined using the Affymetrix EAv3 500 K SNP array and compared to 60 CEPH-derived HapMap (CEU) individuals. 435,632 SNPs overlapped and met annotation criteria in the two groups.

Results
A small but significant global difference in allele frequencies between AJ and CEU was demonstrated by a mean F

ST
of 0.009 (P < 0.001); large regions that differed were found on chromosomes 2 and 6. Haplotype blocks inferred from pairwise linkage disequilibrium (LD) statistics (Haploview) as well as by expectation-maximization haplotype phase inference (HAP) showed a greater number of haplotype blocks in AJ compared to CEU by Haploview (50,397 vs. 44,169) or by HAP (59,269 vs. 54,457). Average haplotype blocks were smaller in AJ compared to CEU (e.g., 36.8 kb vs. 40.5 kb HAP). Analysis of global patterns of local LD decay for closely-spaced SNPs in CEU demonstrated more LD, while for SNPs further apart, LD was slightly greater in the AJ. A likelihood ratio approach showed that runs of homozygous SNPs were approximately 20% longer in AJ. A principal components analysis was sufficient to completely resolve the CEU from the AJ.

Conclusion
LD in the AJ versus was lower than expected by some measures and higher by others. Any putative advantage in whole genome association mapping using the AJ population will be highly dependent on regional LD structure.