bluuebunny/crossref_metadata_2025_split huggingface dataset:
On Bulk Models of Shallow Cumulus Convection
Authors: Bellon Gilles , Stevens Bjorn 
Published: October 2005

Abstract
Two-layer bulk models of the cloudy boundary layer are investigated, focusing on the consistency issues between common assumptions on the turbulent mixing and the thermodynamic profiles. Simplifications of the vertical structure of the conserved variables are shown to lead to inconsistent steady states. First, linear profiles in the cloud layer are incompatible with the common parameterizations of the turbulent mixing. Second, this approximation is inconsistent with simple models of an infinitely thin inversion layer. Simple mass-flux parameterizations of the turbulence are shown to produce reasonable profiles inside the cloud layer without solving the problem of the inversion. The cloud − environment difference and the vertical gradient of the conserved variables appear as interesting test variables for such models, as well as their ability to match the free-tropospheric boundary conditions. The latter certainly requires a unified approach for the cloud and inversion layers.
Predictability and Information Theory. Part II: Imperfect Forecasts
Authors: DelSole Timothy 
Published: October 2005

Abstract
This paper presents a framework for quantifying predictability based on the behavior of imperfect forecasts. The critical quantity in this framework is not the forecast distribution, as used in many other predictability studies, but the conditional distribution of the state given the forecasts, called the regression forecast distribution. The average predictability of the regression forecast distribution is given by a quantity called the mutual information. Standard inequalities in information theory show that this quantity is bounded above by the average predictability of the true system and by the average predictability of the forecast system. These bounds clarify the role of potential predictability, of which many incorrect statements can be found in the literature. Mutual information has further attractive properties: it is invariant with respect to nonlinear transformations of the data, cannot be improved by manipulating the forecast, and reduces to familiar measures of correlation skill when the forecast and verification are joint normally distributed. The concept of potential predictable components is shown to define a lower-dimensional space that captures the full predictability of the regression forecast without loss of generality. The predictability of stationary, Gaussian, Markov systems is examined in detail. Some simple numerical examples suggest that imperfect forecasts are not always useful for joint normally distributed systems since greater predictability often can be obtained directly from observations. Rather, the usefulness of imperfect forecasts appears to lie in the fact that they can identify potential predictable components and capture nonstationary and/or nonlinear behavior, which are difficult to capture by low-dimensional, empirical models estimated from short historical records.
Influence of Western North Pacific Tropical Cyclones on Their Large-Scale Environment
Authors: Sobel Adam H. , Camargo Suzana J. 
Published: October 2005

Abstract
The authors investigate the influence of western North Pacific (WNP) tropical cyclones (TCs) on their large-scale environment by lag regressing various large-scale climate variables [atmospheric temperature, winds, relative vorticity, outgoing longwave radiation (OLR), column water vapor, and sea surface temperature (SST)] on an index of TC activity [accumulated cyclone energy (ACE)] on a weekly time scale. At all leads and lags out to several months, persistent, slowly evolving signals indicative of the El Niño–Southern Oscillation (ENSO) phenomenon are seen in all the variables, reflecting the known seasonal relationship of TCs in the WNP to ENSO. Superimposed on this are more rapidly evolving signals, at leads and lags of one or two weeks, directly associated with the TCs themselves. These include anomalies of positive low-level vorticity, negative OLR, and high column water vapor associated with anomalously positive ACE, found in the region where TCs most commonly form and develop. In the same region, lagging ACE by a week or two and so presumably reflecting the influence of TCs on the local environment, signals are found that might be expected to negatively influence the environment for later cyclogenesis. These signals include an SST reduction in the primary region of TC activity, and a reduction in column water vapor and increase in OLR that may or may not be a result of the SST reduction.
On the same short time scale, an increase in equatorial SST near and east of the date line is seen, presumably associated with equatorial surface westerly anomalies that are also found. This, combined with the correlation between ACE and ENSO indices on the seasonal time scale, suggests the possibility that TCs may play an active role in ENSO dynamics.
Equivalent-Barotropic Definition of Tropospheric Mean Temperature
Authors: Sun Che 
Published: October 2005

Abstract
An equivalent-barotropic (EB) description of the tropospheric temperature field is derived from the geostrophic empirical mode (GEM) in the form of a scalar function Γ(p, ϕ), where p is pressure and ϕ is 300–850-mb thickness. Baroclinic parameter ϕ plays the role of latitude at each longitudinal section. Compared with traditional Eulerian-mean methods, GEM defines a mean field in baroclinic streamfunction space with a time scale much longer than synoptic variability. It prompts an EB concept that is only based on a baroclinic field.
Monthly GEM fields are diagnosed from NCEP–NCAR reanalysis data and account for more than 90% of the tropospheric thermal variance. The circumglobal composite of GEM fields exhibits seasonal, zonal, and hemispheric asymmetries, with larger rms errors occurring in winter and in the Northern Hemisphere (NH). Zonally asymmetric features and planetary deviation from EB are seen in the NH winter GEM. Reconstruction of synoptic sections and correlation analysis reveal that the tropospheric temperature field is EB at the leading order and has a 1-day phase lag behind barotropic variations in extratropical regions.
Impact of Aerosol Intrusions on Arctic Boundary Layer Clouds. Part II: Sea Ice Melting Rates
Authors: Carrió G. G. , Jiang H. , Cotton W. R. 
Published: October 2005

Abstract
The potential impact of intrusions of polluted air into the Arctic basin on sea ice melting rates and the surface energy budget is examined. This paper extends a previous study to cloud-resolving simulations of the entire spring season during the 1998 Surface Heat Budget of the Arctic (SHEBA) field campaign. For that purpose, the Los Alamos National Laboratory sea ice model is implemented into the research and real-time versions of the Regional Atmospheric Modeling System at Colorado State University (RAMS@CSU). This new version of RAMS@CSU also includes a new microphysical module that considers the explicit nucleation of cloud droplets and a bimodal representation of their spectrum. Different aerosol profiles based on 4 May 1998 observations were used to characterize the polluted upper layer and the 2–3 daily SHEBA soundings were utilized to provide time-evolving boundary conditions to the model. Results indicate that entrainment of ice-forming nuclei (IFN) from above the inversion increases the sea ice melting rates when mixed-phase clouds are present. An opposite although less important effect is associated with cloud condensation nuclei (CCN) entrainment when liquid-phase clouds prevail.
Determination of an Amazon Hot Reference Target for the On-Orbit Calibration of Microwave Radiometers
Authors: Brown Shannon T. , Ruf Christopher S. 
Published: October 2005

Abstract
A physically based model is developed to determine hot calibration reference brightness temperatures (TBs) over depolarized regions in the Amazon rain forest. The model can be used to evaluate the end-to-end calibration of any satellite microwave radiometer operating at a frequency between 18 and 40 GHz and angle of incidence between nadir and 55°. The model is constrained by Special Sensor Microwave Imager (SSM/I) TBs measured at 19.35, 22.2, and 37.0 GHz at a 53° angle of incidence and extrapolates/interpolates those measurements to other frequencies and incidence angles. The rms uncertainty in the physically based model is estimated to be 0.57 K. For instances in which coincident SSM/I measurements are not available, an empirical formula has been fit to the physical model to provide hot reference brightness temperature as a function of frequency, incidence angle, time of day, and day of year. The empirical formula has a 0.1-K rms deviation from the physically based model for annual averaged measurements and at most a 0.6-K deviation from the model for any specific time of day or day of year.
Measurements of the Skin Temperature on Small Lakes
Authors: Kurzeja Robert , Pendergast Malcolm , Villa-Aleman Eliel 
Published: October 2005

AbstractAn apparatus to measure the skin temperature and related variables on inland lakes is described. The apparatus is a transparent frame with sensors to measure the skin and bulk water temperature, the wind velocity, and the air temperature and humidity for periods of several days. The sensors are positioned within 1 m of the air–water interface and sample boundary layer variables every 2 s.Data for a 4-h period at midday are discussed, and the vertical fluxes of heat and momentum are calculated using bulk relationships for 1- and 5-min periods. It is shown that the measured water temperature at a depth of 1 cm correlates well with estimates based on the bulk heat flux.The skin temperature depression is calculated from the bulk heat and momentum fluxes and is found to vary between 0.4° and 0.5°C for the 4-h period and was in good agreement with the measured values. However, the calculated and measured skin temperatures were poorly correlated for both the 1- and 5-min averages. This is believed to be due to departures from the steady-state assumptions or to deficiencies in the theory.
Estimation of the Turbulent Fraction in the Free Atmosphere from MST Radar Measurements
Authors: Wilson Richard , Dalaudier Francis , Bertin Francois 
Published: October 2005

Abstract
Small-scale turbulence in the free atmosphere is known to be intermittent in space and time. The turbulence fraction of the atmosphere is a key parameter in order to evaluate the transport properties of small-scale motions and to interpret clear-air radar measurements as well.
Mesosphere–stratosphere–troposphere (MST)/stratosphere–troposphere (ST) radars provide two independent methods for the estimation of energetic parameters of turbulence. First, the Doppler spectral width σ2 is related to the dissipation rate of kinetic energy εk. Second, the radar reflectivity, or C2n, relates to the dissipation rate of available potential energy εp. However, these two measures yield estimates that differ with respect to an important point. The Doppler width measurements, and related εk, are reflectivity-weighted averages. On the other hand, the reflectivity estimate is a volume-averaged quantity. The values of εp depend on both the turbulence intensity and the turbulent fraction within the radar sampling volume.
Now, the two dissipation rates εp and εk are related quantities as shown by various measurements within stratified fluids (atmosphere, ocean, lakes, or laboratory). Therefore, by assuming a “canonical” value for the ratio of dissipation rates, an indirect method is proposed to infer the turbulent fraction from simultaneous radar measurements of reflectivity and Doppler broadening within a sampling volume. This method is checked by using very high resolution radar measurements (30 m and 51 s), obtained by the PROUST radar during a field campaign. The method is found to provide an unbiased estimation of the turbulent fraction, within a factor of 2 or less.
A Preoperational Scheme for Calculating Sea Surface Height by Bernoulli Inverse of Argo Float Data in the North Atlantic
Authors: Alderson Steven G. , Killworth Peter D. 
Published: October 2005

AbstractA preoperational scheme has been implemented to calculate sea surface height fields at 7-day intervals over the North Atlantic. Input data from Argo floats is downloaded and processed in near–real time. The solution method is by Bernoulli inverse. Early results are encouraging. Features of the results are compared with both model and satellite data and show good agreement.
Evaluating the Decomposition of Tropical Atlantic Drifter Observations
Authors: Lumpkin Rick , Garraffo Zulema 
Published: October 2005

Abstract
Because the tropical Atlantic is characterized by regions of strong seasonal variability that have been sampled inhomogeneously by surface drifters, Eulerian averages of these Lagrangian observations in spatially fixed bins may be aliased. In the Pacific, this problem has been circumvented by first calculating seasonal or monthly means. In the Atlantic, such an approach is of limited value because of the relatively sparse database of drifter observations. As an alternative, a methodology is developed in which drifter-observed currents and sea surface temperatures are grouped into bins and, within each bin, simultaneously decomposed into a time-mean, annual and semiannual harmonics, and an eddy residual with a nonzero integral time scale.
The methodology is evaluated using a temporally homogeneous SST product and in situ SST observations, and also using simulated drifter observations in an eddy-resolving model of the Atlantic Ocean. These analyses show that, compared to simple bin averaging, the decomposition developed herein yields significantly improved estimates of time-mean values in regions of strong seasonal variability. The methodology can also successfully estimate the distribution of the seasonal harmonics’ amplitude and phase throughout much of the tropical Atlantic.
Sox4 cooperates with Evi1 in AKXD-23 myeloid tumors via transactivation of proviral LTR
Authors: Boyd Kathryn E. , Xiao Ying-Yi , Fan Kai , Poholek Amanda , Copeland Neal G. , Jenkins Nancy A. , Perkins Archibald S. 
Published: October 2005

AbstractMyeloid leukemias in AKXD23 mice contain proviral insertions at Evi1, resulting in transcriptional activation. Although Evi1 is clearly involved in leukemia, gene transfer studies in mice with Evi1 fail to cause leukemia, arguing that cooperating events are necessary. We reanalyzed AKXD-23 tumors for cooperating proviral insertion and found that each tumor had a proviral insertion in Sox4, which encodes an HMG-box transcription factor. RNA analysis revealed these insertions cause increased Sox4 expression. Overexpression of Sox4 in 32Dcl3 cells markedly inhibited cytokine-induced granulocyte maturation, as documented by morphologic and mRNA analysis. Sox4-expressing cells had higher levels of transcripts associated with proliferation, including Evi1. Conversely, in leukemic cells that express Sox4 and bear provirally activated Evi1, suppression of Sox4 with short hairpin RNAs resulted in down-regulation of both Sox4 and Evi1. By cotransfection studies, Sox4 is able to transactivate the AKV long terminal repeat, which likely explains how Sox4 transcriptionally up-regulates provirally activated Evi1; however, Sox4 does not appear to regulate the native Evi1 promoter. We propose that Sox4 proviral activation is selected for in the setting of prior proviral activation of Evi1, because it transactivates the relatively weak LTR of AKV leading to higher Evi1 expression and consequent block to differentiation. (Blood. 2006;107:733-741)
Monocytes form a vascular barrier and participate in vessel repair after brain injury
Authors: Glod John , Kobiler David , Noel Martha , Koneru Rajeth , Lehrer Shoshana , Medina Daniel , Maric Dragan , Fine Howard A. 
Published: October 2005

AbstractSubpopulations of bone marrow-derived cells can be induced to assume a number of endothelial properties in vitro. However, their ability to form a functional vascular barrier has not been demonstrated. We report that human CD14+ peripheral blood monocytes cultured under angiogenic conditions develop a number of phenotypic and functional properties similar to brain microvascular endothelial cells. These cells express the tight junction proteins zonula occludens 1 (ZO-1) and occludin and form a barrier with a transcellular electrical resistance (TCER) greater than 100 ohm cm2 and low permeability to 4 kDa and 20 kDa dextrans. The TCER of the cellular barrier is decreased by bradykinin and histamine. We also demonstrate that these cells associate with repairing vasculature in areas of brain and skin injury. Our data suggest that CD14+ peripheral blood monocytes participate in the repair of the vascular barrier after brain injury.
Hematopoietic stem cells do not engraft with absolute efficiencies
Authors: Camargo Fernando D. , Chambers Stuart M. , Drew Erin , McNagny Kelly M. , Goodell Margaret A. 
Published: October 2005

AbstractHematopoietic stem cells (HSCs) can be isolated from murine bone marrow by their ability to efflux the Hoechst 33342 dye. This method defines an extremely small and hematopoietically potent subset of cells known as the side population (SP). Recent studies suggest that transplanted single SP cells are capable of lymphohematopoietic repopulation at near absolute efficiencies. Here, we carefully reevaluate the hematopoietic potential of individual SP cells and find substantially lower rates of reconstitution. Our strategy involved the cotransplantation of single SP cells along with different populations of competitor cells that varied in their self-renewal capacity. Even with minimized HSC competition, SP cells were only able to reconstitute up to 35% of recipient mice. Furthermore, through immunophenotyping and clonal in vitro assays we find that SP cells are virtually homogeneous. Isolation of HSCs on the basis of Hoechst exclusion and a single cell-surface marker allows enrichment levels similar to that obtained with complex multicolor strategies. Altogether, our results indicate that even an extremely homogeneous HSC population, based on phenotype and dye efflux, cannot reconstitute mice at absolute efficiencies.
Erythropoietin stimulates phosphorylation and activation of GATA-1 via the PI3-kinase/AKT signaling pathway
Authors: Zhao Wei , Kitidis Claire , Fleming Mark D. , Lodish Harvey F. , Ghaffari Saghi 
Published: October 2005

AbstractErythropoietin (Epo) stimulation of its receptor's downstream signaling pathways and optimum function of GATA-1 transcription factor are both essential for normal erythroid cell development. Epo-receptor (EpoR) signaling and GATA-1 regulate proliferation, survival, differentiation, and maturation of erythroid cells. Whether any signal that is generated by EpoR targets GATA-1 or affects GATA-1 transcriptional activity is not known. Here, we demonstrate that stimulation of EpoR results in phosphorylation of GATA-1 at serine 310 (S310) in primary fetal liver erythroid progenitors and in cultured erythroid cells. We show that phosphorylation of GATA-1 is important for Epo-induced maturation of fetal liver erythroid progenitor cells. The PI3-kinase/AKT signaling pathway is identified as a mediator of Epo-induced phosphorylation of GATA-1. AKT serine threonine kinase phosphorylates GATA-1S310 in vitro and in erythroid cells and enhances GATA-1 transcriptional activity. These data demonstrate that EpoR signaling phosphorylates GATA-1 and modulates its activity via the PI3-kinase/AKT signaling pathway.
In silico characterization of the family of PARP-like poly(ADP-ribosyl)transferases (pARTs)
Authors: Otto Helge , Reche Pedro A , Bazan Fernando , Dittmar Katharina , Haag Friedrich , Koch-Nolte Friedrich 
Published: October 2005

Abstract

Background
ADP-ribosylation is an enzyme-catalyzed posttranslational protein modification in which mono(ADP-ribosyl)transferases (mARTs) and poly(ADP-ribosyl)transferases (pARTs) transfer the ADP-ribose moiety from NAD onto specific amino acid side chains and/or ADP-ribose units on target proteins.

Results
Using a combination of database search tools we identified the genes encoding recognizable pART domains in the public genome databases. In humans, the pART family encompasses 17 members. For 16 of these genes, an orthologue exists also in the mouse, rat, and pufferfish. Based on the degree of amino acid sequence similarity in the catalytic domain, conserved intron positions, and fused protein domains, pARTs can be divided into five major subgroups. All six members of groups 1 and 2 contain the H-Y-E trias of amino acid residues found also in the active sites of Diphtheria toxin and Pseudomonas exotoxin A, while the eleven members of groups 3 – 5 carry variations of this motif. The pART catalytic domain is found associated in Lego-like fashion with a variety of domains, including nucleic acid-binding, protein-protein interaction, and ubiquitylation domains. Some of these domain associations appear to be very ancient since they are observed also in insects, fungi, amoebae, and plants. The recently completed genome of the pufferfish T. nigroviridis contains recognizable orthologues for all pARTs except for pART7. The nearly completed albeit still fragmentary chicken genome contains recognizable orthologues for twelve pARTs. Simpler eucaryotes generally contain fewer pARTs: two in the fly D. melanogaster, three each in the mosquito A. gambiae, the nematode C. elegans, and the ascomycete microfungus G. zeae, six in the amoeba E. histolytica, nine in the slime mold D. discoideum, and ten in the cress plant A. thaliana. GenBank contains two pART homologues from the large double stranded DNA viruses Chilo iridescent virus and Bacteriophage Aeh1 and only a single entry (from V. cholerae) showing recognizable homology to the pART-like catalytic domains of Diphtheria toxin and Pseudomonas exotoxin A.

Conclusion
The pART family, which encompasses 17 members in the human and 16 members in the mouse, can be divided into five subgroups on the basis of sequence similarity, phylogeny, conserved intron positions, and patterns of genetically fused protein domains.