bluuebunny/crossref_metadata_2025_split huggingface dataset:
Some Influences of Background Flow Conditions on the Generation of Turbulence due to Gravity Wave Breaking above Deep Convection
Authors: Lane Todd P. , Sharman Robert D. 
Published: April 2008

Abstract
Deep moist convection generates turbulence in the clear air above and around developing clouds, penetrating convective updrafts and mature thunderstorms. This turbulence can be due to shearing instabilities caused by strong flow deformations near the cloud top, and also to breaking gravity waves generated by cloud–environment interactions. Turbulence above and around deep convection is an important safety issue for aviation, and improved understanding of the conditions that lead to out-of-cloud turbulence formation may result in better turbulence avoidance guidelines or forecasting capabilities. In this study, a series of high-resolution two- and three-dimensional model simulations of a severe thunderstorm are conducted to examine the sensitivity of above-cloud turbulence to a variety of background flow conditions—in particular, the above-cloud wind shear and static stability. Shortly after the initial convective overshoot, the above-cloud turbulence and mixing are caused by local instabilities in the vicinity of the cloud interfacial boundary. At later times, when the convection is more mature, gravity wave breaking farther aloft dominates the turbulence generation. This wave breaking is caused by critical-level interactions, where the height of the critical level is controlled by the above-cloud wind shear. The strength of the above-cloud wind shear has a strong influence on the occurrence and intensity of above-cloud turbulence, with intermediate shears generating more extensive regions of turbulence, and strong shear conditions producing the most intense turbulence. Also, more stable above-cloud environments are less prone to turbulence than less stable situations. Among other things, these results highlight deficiencies in current turbulence avoidance guidelines in use by the aviation industry.
A Moist Benchmark Calculation for Atmospheric General Circulation Models
Authors: Lee Myong-In , Suarez Max J. , Kang In-Sik , Held Isaac M. , Kim Daehyun 
Published: April 2008

Abstract
A benchmark calculation is designed to compare the climate and climate sensitivity of atmospheric general circulation models (AGCMs). The experimental setup basically follows that of the aquaplanet experiment (APE) proposed by Neale and Hoskins, but a simple mixed layer ocean is embedded to enable air–sea coupling and the prediction of surface temperature. In calculations with several AGCMs, this idealization produces very strong zonal-mean flow and exaggerated ITCZ strength, but the model simulations remain sufficiently realistic to justify the use of this framework in isolating key differences between models. Because surface temperatures are free to respond to model differences, the simulation of the cloud distribution, especially in the subtropics, affects many other aspects of the simulations. The analysis of the simulated tropical transients highlights the importance of convection inhibition and air–sea coupling as affected by the depth of the mixed layer. These preliminary comparisons demonstrate that this idealized benchmark provides a discriminating framework for understanding the implications of differing physics parameterization in AGCMs.
Analysis of Atmospheric Energy Transport in ERA-40 and Implications for Simple Models of the Mean Tropical Circulation
Authors: Peters Matthew E. , Kuang Zhiming , Walker Christopher C. 
Published: April 2008

Abstract
An analysis of atmospheric energy transport in 22 years (1980–2001) of the 40-yr ECMWF Re-Analysis (ERA-40) is presented. In the analyzed budgets, there is a large cancellation between divergences of dry static and latent energy such that the total energy divergence is positive over all tropical oceanic regions except for the east Pacific cold tongue, consistent with previous studies. The west Pacific and Indian Oceans are characterized by a balance between diabatic sources and mean advective energy export, with a small eddy contribution. However, in the central and eastern Pacific convergence zone, total energy convergence by the mean circulation is balanced by submonthly eddies, with a small diabatic source. Decomposing the mean advective tendency into terms due to horizontal and vertical advection shows that the spatial variation in the mean advection is due largely to variations in vertical advection; these variations are further attributed to variations in the vertical profile of the vertical velocity. The eddy energy export, due almost exclusively to eddy moisture export, does not exhibit any significant seasonal variation.
The relationship between the eddies and the mean circulation is examined. Large-scale moisture diffusion is correlated with eddy moisture export on (500 km)2 spatial scales, implying that eddy activity preferentially dries narrow convergence zones over wide ones. Eddy moisture export is further linked to the depth of mean convection in large-scale convergence zones with larger eddy export associated with shallower circulations. This suggests a mechanism that could contribute to the observed variation in mean divergence profiles across the northern tropical Pacific whereby sea surface temperature gradients set the width of convergence zones and eddy activity modulates the tropospheric relative humidity and divergence profile. The importance of variations in the vertical profile of the vertical velocity and eddies in closing the energy budget implies that simple models of the mean tropical circulation should include these effects.
Recent Changes in Surface Humidity: Development of the HadCRUH Dataset
Authors: Willett Katharine M. , Jones Philip D. , Gillett Nathan P. , Thorne Peter W. 
Published: April 2008

Abstract
Water vapor constitutes the most significant greenhouse gas, is a key driver of many atmospheric processes, and hence, is fundamental to understanding the climate system. It is a major factor in human “heat stress,” whereby increasing humidity reduces the ability to stay cool. Until now no truly global homogenized surface humidity dataset has existed with which to assess recent changes. The Met Office Hadley Centre and Climatic Research Unit Global Surface Humidity dataset (HadCRUH), described herein, provides a homogenized quality controlled near-global 5° by 5° gridded monthly mean anomaly dataset in surface specific and relative humidity from 1973 to 2003. It consists of land and marine data, and is geographically quasi-complete over the region 60°N–40°S.
Between 1973 and 2003 surface specific humidity has increased significantly over the globe, tropics, and Northern Hemisphere. Global trends are 0.11 and 0.07 g kg−1 (10 yr)−1 for land and marine components, respectively. Trends are consistently larger in the tropics and in the Northern Hemisphere during summer, as expected: warmer regions exhibit larger increases in specific humidity for a given temperature change under conditions of constant relative humidity, based on the Clausius–Clapeyron equation. Relative humidity trends are not significant when averaged over the landmass of the globe, tropics, and Northern Hemisphere, although some seasonal changes are significant.
A strong positive bias is apparent in marine humidity data prior to 1982, likely owing to a known change in reporting practice for dewpoint temperature at this time. Consequently, trends in both specific and relative humidity are likely underestimated over the oceans.
Comparison of FASST and SNTHERM in Three Snow Accumulation Regimes
Authors: Frankenstein Susan , Sawyer Anne , Koeberle Julie 
Published: April 2008

AbstractNumerical experiments of snow accumulation and depletion were carried out as well as surface energy fluxes over four Cold Land Processes Experiment (CLPX) sites in Colorado using the Snow Thermal model (SNTHERM) and the Fast All-Season Soil Strength model (FASST). SNTHERM is a multilayer snow model developed to describe changes in snow properties as a function of depth and time, using a one-dimensional mass and energy balance. The model is intended for seasonal snow covers and addresses conditions found throughout the winter, from initial ground freezing in the fall to snow ablation in the spring. It has been used by many researchers over a variety of terrains. FASST is a newly developed one-dimensional dynamic state-of-the-ground model. It calculates the ground’s moisture content, ice content, temperature, and freeze–thaw profiles as well as soil strength and surface ice and snow accumulation/depletion. Because FASST is newer and not as well known, the authors wanted to determine its use as a snow model by comparing it with SNTHERM, one of the most established snow models available. It is demonstrated that even though FASST is only a single-layer snow model, the RMSE snow depth compared very favorably against SNTHERM, often performing better during the accumulation phase. The surface energy fluxes calculated by the two models were also compared and were found to be similar.
Comparing Simulated and Measured Sensible and Latent Heat Fluxes over Snow under a Pine Canopy to Improve an Energy Balance Snowmelt Model
Authors: Marks D. , Winstral A. , Flerchinger G. , Reba M. , Pomeroy J. , Link T. , Elder K. 
Published: April 2008

AbstractDuring the second year of the NASA Cold Land Processes Experiment (CLPX), an eddy covariance (EC) system was deployed at the Local Scale Observation Site (LSOS) from mid-February to June 2003. The EC system was located beneath a uniform pine canopy, where the trees are regularly spaced and are of similar age and height. In an effort to evaluate the turbulent flux calculations of an energy balance snowmelt model (SNOBAL), modeled and EC-measured sensible and latent heat fluxes between the snow cover and the atmosphere during this period are presented and compared. Turbulent fluxes comprise a large component of the snow cover energy balance in the premelt and ripening period (March–early May) and therefore control the internal energy content of the snow cover as melt accelerates in late spring. Simulated snow cover depth closely matched measured values (RMS difference 8.3 cm; Nash–Sutcliff model efficiency 0.90), whereas simulated snow cover mass closely matched the few measured values taken during the season. Over the 927-h comparison period using the default model configuration, simulated sensible heat H was within 1 W m−2, latent heat LυE within 4 W m−2, and cumulative sublimation within 3 mm of that measured by the EC system. Differences between EC-measured and simulated fluxes occurred primarily at night. The reduction of the surface layer specification in the model from 25 to 10 cm reduced flux differences between EC-measured and modeled fluxes to 0 W m−2 for H, 2 W m−2 for LυE, and 1 mm for sublimation. When only daytime fluxes were compared, differences were further reduced to 1 W m−2 for LυE and &lt;1 mm for sublimation. This experiment shows that in addition to traditional mass balance methods, EC-measured fluxes can be used to diagnose the performance of a snow cover energy balance model. It also demonstrates the use of eddy covariance methods for measuring heat and mass fluxes from snow covers at a low-wind, below-canopy site.
The Potential Impact of Using Persistence as a Reference Forecast on Perceived Forecast Skill
Authors: Mittermaier Marion P. 
Published: April 2008

Abstract
Skill is defined as actual forecast performance relative to the performance of a reference forecast. It is shown that the choice of reference (e.g., random or persistence) can affect the perceived performance of the forecast system. Two scores, the equitable threat score (ETS) and the odds ratio benefit skill score (ORBSS), were chosen to show the impact of using a persistence forecast, first using some simple hypothetical scenarios and second for actual forecasts from the Met Office Unified Model (UM) of precipitation, total cloud cover, and visibility during 2006. Overall persistence offers a sterner test of true forecast added value and accuracy, but using a more realistic reference may come at a cost. Using persistence introduces an additional degree of freedom to the skill assessment, which may be rather variable for “weather parameters.” Ultimately, the aim of any forecasting system should be to achieve a substantive separation between the inherent skill of the reference (which represents basic predictability) and the actual forecast.
Unrelated donor transplants in adults with Philadelphia-negative acute lymphoblastic leukemia in first complete remission
Authors: Marks David I. , Pérez Waleska S. , He Wensheng , Zhang Mei-Jie , Bishop Michael R. , Bolwell Brian J. , Bredeson Christopher N. , Copelan Edward A. , Gale Robert Peter , Gupta Vikas , Hale Gregory A. , Isola Luis M. , Jakubowski Ann A. , Keating Armand , Klumpp Thomas R. , Lazarus Hillard M. , Liesveld Jane L. , Maziarz Richard T. , McCarthy Philip L. , Sabloff Mitchell , Schiller Gary , Sierra Jorge , Tallman Martin S. , Waller Edmund K. , Wiernik Peter H. , Weisdorf Daniel J. 
Published: April 2008

Abstract
We report the retrospective outcomes of unrelated donor (URD) transplants in 169 patients with acute lymphoblastic leukemia (ALL) in first complete remission (CR1) who received transplants between 1995 and 2004. Median age was 33 years (range, 16-59 years). A total of 50% had a white blood cell count (WBC) more than 30 × 109/L, 18% extramedullary disease, 42% achieved CR more than 8 weeks from diagnosis, 25% had adverse cytogenetics, and 19% had T-cell leukemia. A total of 41% were HLA well-matched, 41% partially matched with their donors, and 18% were HLA-mismatched. At 54-month median follow-up, incidences of acute grade 2-IV, III to IV, and chronic graft-versus-host disease were 50%, 25%, and 43%, respectively. Five-year treatment-related mortality (TRM), relapse, and overall survival were 42%, 20%, and 39%, respectively. In multivariate analyses, TRM was significantly higher with HLA-mismatched donors and T-cell depletion. Relapse risk was higher if the diagnostic WBC was more than 100 × 109/L. Factors associated with poorer survival included WBC more than 100 × 109/L, more than 8 weeks to CR1, cytomegalovirus seropositivity, HLA mismatching, and T-cell depletion. Nearly 40% of adults with ALL in CR1 survive 5 years after URD transplantation. Relapse risks were modest; TRM is the major cause of treatment failure. Selecting closely HLA-matched URD and reducing TRM should improve results.
Comparative transcriptome analysis of Arabidopsis thaliana infested by diamond back moth (Plutella xylostella) larvae reveals signatures of stress response, secondary metabolism, and signalling
Authors: Ehlting Jürgen , Chowrira Sunita G , Mattheus Nathalie , Aeschliman Dana S , Arimura Gen-Ichiro , Bohlmann Jörg 
Published: April 2008

Abstract

Background
Plants are exposed to attack from a large variety of herbivores. Feeding insects can induce substantial changes of the host plant transcriptome. Arabidopsis thaliana has been established as a relevant system for the discovery of genes associated with response to herbivory, including genes for specialized (i.e. secondary) metabolism as well as genes involved in plant-insect defence signalling.

Results
Using a 70-mer oligonulceotide microarray covering 26,090 gene-specific elements, we monitored changes of the Arabidopsis leaf transcriptome in response to feeding by diamond back moth (DBM; Plutella xylostella) larvae. Analysis of samples from a time course of one hour to 24 hours following onset of DBM feeding revealed almost three thousand (2,881) array elements (including 2,671 genes with AGI annotations) that were differentially expressed (>2-fold; p[t-test] < 0.05) of which 1,686 also changed more than twofold in expression between at least two time points of the time course with p(ANOVA) < 0.05. While the majority of these transcripts were up-regulated within 8 h upon onset of insect feeding relative to untreated controls, cluster analysis identified several distinct temporal patterns of transcriptome changes. Many of the DBM-induced genes fall into ontology groups annotated as stress response, secondary metabolism and signalling. Among DBM-induced genes associated with plant signal molecules or phytohormones, genes associated with octadecanoid signalling were clearly overrepresented. We identified a substantial number of differentially expressed genes associated with signal transduction in response to DBM feeding, and we compared there expression profiles with those of previously reported transcriptome responses induced by other insect herbivores, specifically Pieris rapae, Frankliniella occidentalis, Bemisia tabaci,Myzus persicae, and Brevicoryne brassicae.

Conclusion
Arabidopsis responds to feeding DBM larvae with a drastic reprogramming of the transcriptome, which has considerable overlap with the response induced by other insect herbivores. Based on a meta-analysis of microarray data we identified groups of transcription factors that are either affected by multiple forms of biotic or abiotic stress including DBM feeding or, alternatively, were responsive to DBM herbivory but not to most other forms of stress.
Detailed characterization of the mouse embryonic stem cell transcriptome reveals novel genes and intergenic splicing associated with pluripotency
Authors: Kunarso Galih , Wong Kee-Yew , Stanton Lawrence W , Lipovich Leonard 
Published: April 2008

AbstractBackgroundTranscriptional control of embryonic stem (ES) cell pluripotency has been a subject of intense study. Transcriptional regulators including Oct4 (Oct3/4 index), Sox2 and Nanog are fundamental for maintaining the undifferentiated state. However, the ES cell transcriptome is not limited to their targets, and exhibits considerable complexity when assayed with microarray, MPSS, cDNA/EST sequencing, and SAGE technologies. To identify novel genes associated with pluripotency, we globally searched for ES transcripts not corresponding to known genes, validated their sequences, determined their expression profiles, and employed RNAi to test their function.ResultsGene Identification Signature (GIS) analysis, a SAGE derivative distinguished by paired 5' and 3' transcript end tags, identified 153 candidate novel transcriptional units (TUs) distinct from known genes in a mouse E14 ES mRNA library. We focused on 16 TUs free of artefacts and mapping discrepancies, five of which were validated by RTPCR product sequencing. Two of the TUs were revealed by annotation to represent novel protein-coding genes: a PRY-domain cluster member and a KRAB-domain zinc finger. The other three TUs represented intergenic splicing events involving adjacent, functionally unrelated protein-coding genes transcribed in the same orientation, with one event potentially encoding a fusion protein containing domains from both component genes (Clk2 and Scamp3). Expression profiling using embryonic samples and adult tissue panels confirmed that three of the TUs were unique to or most highly expressed in ES cells. Expression levels of all five TUs dropped dramatically during three distinct chemically induced differentiation treatments of ES cells in culture. However, siRNA knockdowns of the TUs did not alter mRNA levels of pluripotency or differentiation markers, and did not affect cell morphology.ConclusionTranscriptome libraries retain considerable potential for novel gene discovery despite massive recent cDNA and EST sequencing efforts; cDNA and EST evidence for these ES cell TUs had been limited or absent. RTPCR and full-length sequencing remain essential in resolving the bottleneck between numerous candidate novel transcripts inferred from high-throughput sequencing and the small fraction that can be validated. RNAi results indicate that, despite their strong association with pluripotency, these five transcriptomic novelties may not be required for maintaining it.
Altered regulation of Prox1-gene-expression in liver tumors
Authors: Dudas Jozsef , Mansuroglu Tümen , Moriconi Federico , Haller Florian , Wilting Joerg , Lorf Thomas , Füzesi Laszlo , Ramadori Giuliano 
Published: April 2008

Abstract

Background
Prospero-related homeobox 1 (Prox1) transcription factor was described as a tumor-suppressor gene in liver tumors. In contrast, Prox1 knock out in murine embryos drastically reduces proliferation of hepatoblasts.

Methods
We have studied the expression of Prox1 in normal liver, liver cirrhosis and peritumoral liver samples in comparison to hepatocellular (HCC) and cholangiocellular carcinoma (CCC) at mRNA, protein and functional levels.

Results
Prox1 was found in hepatocytes of normal liver, while normal bile duct epithelial cells were negative. However, Prox1+ cells, which co-expressed biliary epithelial makers and showed ductular morphology, could be detected within fibrotic septa of cirrhotic livers, and in both HCC and CCC. Two Prox1 mRNA isoforms (2.9 kb and 7.9 kb) were identified with a prevalence of the longer isoform in several HCC samples and the shorter in most CCC samples. Evidence was provided that Myc-associated zinc finger protein (MAZ) might significantly contribute to the gene expression of Prox1 in HCC, while neo-expression of Prox1 in CCC remains to be resolved. A point mutation in the prospero domain of Prox1 was found in one HCC sample.

Conclusion
Our study shows dysregulation of Prox1 in liver cirrhosis, HCC and CCC, such as neo-expression in cells with biliary epithelial phenotype in liver cirrhosis, and in CCC. Altered Prox1 mRNA expression is partly regulated by MAZ, and mutation of the prospero domain in HCC indicates an involvement for Prox1 during tumor progression.
Socioeconomic position and risk of short-term weight gain: Prospective study of 14,619 middle-aged men and women
Authors: Purslow Lisa R , Young Elizabeth H , Wareham Nicholas J , Forouhi Nita , Brunner Eric J , Luben Robert N , Welch Ailsa A , Khaw Kay-Tee , Bingham Shelia A , Sandhu Manjinder S 
Published: April 2008

Abstract

Background
The association between socioeconomic position in middle age and risk of subsequent, short-term weight gain is unknown. We therefore assessed this association in a prospective population based cohort study in Norfolk, UK.

Methods
We analysed data on 14,619 middle-aged men and women (aged between 40–75 at baseline) with repeated objective measures of weight and height at baseline (1993–1997) and follow up (1998–2000).

Results
During follow up 5,064 people gained more than 2.5 kg. Compared with the highest social class, individuals in the lowest social class had around a 30% greater risk of gaining more than 2.5 kg (OR 1.29; 95% CI 1.11–1.51; p for trend = 0.002). This association remained statistically significant following adjustment for sex, age, baseline BMI, smoking, and follow up time (OR 1.25; CI 1.07–1.46; p for trend <0.001). We also found no material difference between unadjusted models and those including all confounders and potential mediators.

Conclusion
Individuals of low socioeconomic position are at greatest risk of gaining weight during middle age, which is not explained by classical correlates of socioeconomic position and risk factors for obesity.