bluuebunny/crossref_metadata_2025_split huggingface dataset:
Implications of Both Statistical Equilibrium and Global Warming Simulations with CCSM3. Part I: On the Decadal Variability in the North Pacific Basin
Authors: d’Orgeville Marc , Peltier W. Richard 
Published: May 2009

Abstract
In the low-resolution version of the Community Climate System Model, version 3 (CCSM3), the modeled North Pacific decadal variability is demonstrated to be independent of the epoch for which a statistically steady control simulation is constructed, either preindustrial or modern; however, it is demonstrated to be significantly affected by the different global warming scenarios investigated.
In the control simulations, the North Pacific basin is shown to be dominated by sea surface temperature (SST) variability with a time scale of approximately 20 yr. This mode of variability is in close accord with the observed characteristics of the Pacific decadal oscillation (PDO). A detailed analysis of the statistical equilibrium runs is performed based on other model variables as well [sea surface salinity (SSS), barotropic circulation, freshwater and heat fluxes, wind stress curl, sea ice, and snow coverage]. These analyses confirm that the underlying mechanism of the PDO involves a basin-scale mode of ocean adjustment to changes of the atmospheric forcing associated with the Aleutian low pressure system. However, they also suggest that the observed sign reversal of the PDO arises from a feedback in the northern part of the basin. In this novel hypothesis, the advection to the Bering Sea of “spice” anomalies formed in the central and western Pacific sets up a typical 10-yr time scale for the triggering of the PDO reversal.
In all of the global warming simulations described in this paper, the signal represented by the detrended SST variability in the North Pacific displays significant power at multidecadal frequencies. In these simulations, the natural North Pacific decadal variability, as characterized in the control simulations (the PDO), remains the leading mode of variability only for moderate forcing. If the warming is too strong, then the typical 20-yr time scale of the canonical PDO can no longer be detected, except in terms of SSS variability and only prior to a significant change that occurs in the Bering Strait Throughflow.
Implications of Both Statistical Equilibrium and Global Warming Simulations with CCSM3. Part II: On the Multidecadal Variability in the North Atlantic Basin
Authors: d’Orgeville Marc , Peltier W. Richard 
Published: May 2009

Abstract
The nature of the multidecadal variability in the North Atlantic basin is investigated through detailed analysis of multicentury integrations performed using the low-resolution version of the Community Climate System Model, version 3 (CCSM3), a modern atmosphere–ocean coupled general circulation model. Specifically, the results of control simulations under both preindustrial and present-day perpetual seasonal cycle conditions are compared to each other and also to the results of five simulations with increasing CO2 concentration scenarios.
In the absence of greenhouse gas–induced warming, the meridional overturning circulation (MOC) variability is shown to be dependent on the details of the simulation. In the present-day control simulation, the MOC is characterized by a broad spectrum of low frequencies, whereas, in preindustrial control simulations, MOC variability is characterized either by a well-defined periodicity of 60 yr or by a broad spectrum of low frequencies. In all the control simulations, the MOC appears to respond with a delay of 10 yr to synchronous temperature and salinity anomalies in the deep water formation sites located in the subpolar gyre, but salinity dominates the density anomalies. The explanation of the modeled MOC periodicity is therefore sought in the creation of these density anomalies. The influence of increased sea ice coverage under cold/preindustrial conditions is shown to modify the salinity variability, but it is not a sufficient condition for the support of the MOC periodicity. Instead, its source appears to be a modified subpolar gyre circulation resulting from interaction with the bottom bathymetry, which is able to sustain strong coupling between the horizontal and overturning circulations.
Based on the global warming analyses, for the simulations initialized from the cold/preindustrial statistical equilibrium run, the North Atlantic variability continues to be dominated by strong coupling between the horizontal and overturning circulations if the imposed forcing is weak. More generally, the delayed response of the MOC to surface density anomalies in the deep water formation regions is preserved under weak forcing.
Estimating the Proportion of Monthly Precipitation that Falls in Solid Form
Authors: Legates David R. , Bogart Tianna A. 
Published: May 2009

Abstract
In applications where a monthly temporal resolution is employed, an important variable is the proportion of monthly precipitation that falls in solid form. Globally applicable equations for estimating this variable developed by previously published research are reevaluated. A revised equation developed 20 years ago by the lead author for climatological analysis works well for long-term data but not for actual monthly averages. A new equation, therefore, is developed for use with monthly data using an Arctic database of stations above 50°N latitude. These two equations have mean absolute fit errors of 0.0569 and 0.0614, respectively. The data were split into four regions—North America, northern Europe, northern Asia, and Greenland—and were also evaluated for the effect of elevation or seasonality influences. Results suggest that seasonality also is an important variable, particularly to differentiate between midwinter and transition months (i.e., October and April).
A Theory-Based Hydrometeor Identification Algorithm for X-Band Polarimetric Radars
Authors: Dolan Brenda , Rutledge Steven A. 
Published: May 2009

Abstract
Although much work has been done at S band to automatically identify hydrometeors by using polarimetric radar, several challenges are presented when adapting such algorithms to X band. At X band, attenuation and non-Rayleigh scattering can pose significant problems. This study seeks to develop a hydrometeor identification (HID) algorithm for X band based on theoretical simulations using the T-matrix scattering model of seven different hydrometeor types: rain, drizzle, aggregates, pristine ice crystals, low-density graupel, high-density graupel, and vertical ice. Hail and mixed-phase hydrometeors are excluded for the purposes of this study. Non-Rayleigh scattering effects are explored by comparison with S-band simulations. Variable ranges based on the theoretical simulations are used to create one-dimensional fuzzy-logic membership beta functions that form the basis of the new X-band HID. The theory-based X-band HID is applied to a case from the Collaborative Adaptive Sensing of the Atmosphere (CASA) Integrated Project 1 (IP1) network of X-band radars, and comparisons are made with similar S-band hydrometeor identification algorithms applied to data from the S-band polarimetric Next Generation Weather Radar (NEXRAD) prototype radar, KOUN. The X-band HID shows promise for illustrating bulk hydrometeor types and qualitatively agrees with analysis from KOUN. A simple reflectivity- and temperature-only HID is also applied to both KOUN and CASA IP1 data to reveal benefits of the polarimetric-based HID algorithms, especially in the classification of ice hydrometeors and oriented ice crystals.
Portable Raman Lidar PollyXT for Automated Profiling of Aerosol Backscatter, Extinction, and Depolarization
Authors: Althausen Dietrich , Engelmann Ronny , Baars Holger , Heese Birgit , Ansmann Albert , Müller Detlef , Komppula Mika 
Published: May 2009

Abstract
Two versions of the portable aerosol Raman lidar system (Polly) are presented. First, the two-channel prototype is depicted. It has been developed for the independent and simultaneous determination of particle backscatter and extinction coefficient profiles at 532 nm. Second, the 3 + 2 Raman lidar PollyXT (3 + 2: three backscatter and two extinction coefficients), the second generation of Polly, is described. The extended capabilities of PollyXT are due to the simultaneous emission of light with three wavelengths, more laser power, a larger main receiver mirror, and seven receiver channels. These systems are completely remotely controlled and all measurements are performed automatically. The collected data are transferred to a home server via the Internet and are displayed on a Web page. This paper describes the details of the optical setup, the housekeeping of the systems, and the used data retrieval routines. A measurement example taken close to Manaus, Brazil, on 15 August 2008 shows the capabilities of PollyXT.
On the Weighting of Multimodel Ensembles in Seasonal and Short-Range Weather Forecasting
Authors: Casanova Sophie , Ahrens Bodo 
Published: May 2009

Abstract
The performance of multimodel ensemble forecasting depends on the weights given to the different models of the ensemble in the postprocessing of the direct model forecasts. This paper compares the following different weighting methods with or without taking into account the single-model performance: equal weighting of models (EW), simple skill-based weighting (SW), using a simple model performance indicator, and weighting by Bayesian model averaging (BMA). These methods are tested for both short-range weather and seasonal temperature forecasts. The prototype seasonal multimodel ensemble is the Development of a European Multimodel Ensemble System for Seasonal-to-Interannual Prediction (DEMETER) system, with four different models and nine forecasts per model. The short-range multimodel prototype system is the European Meteorological Services (EUMETNET) Poor-Man’s Ensemble Prediction System (PEPS), with 14 models and one forecast per model. It is shown that despite the different forecast ranges and spatial scales, the impact of weighting is comparable for both forecast systems and is related to the same ensemble characteristics. In both cases the added value of ensemble forecasting over single-model forecasting increases considerably with the decreasing correlation of the models’ forecast errors, with a relation depending only on the number of models. Also, in both cases a larger spread in model performance increases the added value of combining model forecasts using the performance-based SW or BMA weighting instead of EW. Finally, the more complex BMA weighting adds value over SW only if the best model performs better than the ensemble with EW weighting.
Differential expression of NADPH oxidases in megakaryocytes and their role in polyploidy
Authors: McCrann Donald J. , Eliades Alexia , Makitalo Maria , Matsuno Kuniharu , Ravid Katya 
Published: May 2009

Abstract
Megakaryocytes (MKs) undergo an endomitotic cell cycle, leading to polyploidy. We examined the expression of the flavoproteins and oxidative stress-promoting enzymes, NADPH oxidases (Nox's), in MKs because of their known role in promoting the cell cycle. Although the expression of Nox isoforms varies between cell types, they are induced at the mRNA level by mitogenic stimuli. Western blotting or reverse transcription–polymerase chain reaction of purified mouse MKs isolated from thrombopoietin (TPO)–treated bone marrow (BM) cultures indicated high expression of Nox1, a weak expression of Nox4, and no significant expression of Nox2. Immunofluorescence of freshly isolated MKs confirmed strong expression of Nox1 in one-third of MKs, whereas Nox1 staining was detected in nearly all MKs in TPO-stimulated BM cultures. Treatment of mouse BM cultures with Nox inhibitors resulted in accumulation of MKs with low DNA content levels and significant reduction of higher ploidy MKs. Purified, Nox-inhibited MKs showed a notable decrease in the level of the G1 phase cyclin E, a cyclin associated with MK polyploidy, and its up-regulation restored most of the effect of Nox inhibitors. Hence, this study shows the expression of Nox isoforms in MKs and highlights a potential role of flavoproteins in promoting polyploidization in this lineage.
Apoptosis signal-regulating kinase 1 mediates denbinobin-induced apoptosis in human lung adenocarcinoma cells
Authors: Kuo Chen-Tzu , Chen Bing-Chang , Yu Chung-Chi , Weng Chih-Ming , Hsu Ming-Jen , Chen Chien-Chih , Chen Mei-Chieh , Teng Che-Ming , Pan Shiow-Lin , Bien Mauo-Ying , Shih Chung-Hung , Lin Chien-Huang 
Published: May 2009

Abstract
In the present study, we explore the role of apoptosis signal-regulating kinase 1 (ASK1) in denbinobin-induced apoptosis in human lung adenocarcinoma (A549) cells. Denbinobin-induced cell apoptosis was attenuated by an ASK1 dominant-negative mutant (ASK1DN), two antioxidants (N-acetyl-L-cysteine (NAC) and glutathione (GSH)), a c-Jun N-terminal kinase (JNK) inhibitor (SP600125), and an activator protein-1 (AP-1) inhibitor (curcumin). Treatment of A549 cells with denbinobin caused increases in ASK1 activity and reactive oxygen species (ROS) production, and these effects were inhibited by NAC and GSH. Stimulation of A549 cells with denbinobin caused JNK activation; this effect was markedly inhibited by NAC, GSH, and ASK1DN. Denbinobin induced c-Jun phosphorylation, the formation of an AP-1-specific DNA-protein complex, and Bim expression. Bim knockdown using a bim short interfering RNA strategy also reduced denbinobin-induced A549 cell apoptosis. The denbinobin-mediated increases in c-Jun phosphorylation and Bim expression were inhibited by NAC, GSH, SP600125, ASK1DN, JNK1DN, and JNK2DN. These results suggest that denbinobin might activate ASK1 through ROS production to cause JNK/AP-1 activation, which in turn induces Bim expression, and ultimately results in A549 cell apoptosis.
Molecular characterization of a fungal gene paralogue of the penicillin penDE gene of Penicillium chrysogenum
Authors: García-Estrada Carlos , Vaca Inmaculada , Ullán Ricardo V , van den Berg Marco A , Bovenberg Roel AL , Martín Juan Francisco 
Published: May 2009

Abstract

Background

Penicillium chrysogenum converts isopenicillin N (IPN) into hydrophobic penicillins by means of the peroxisomal IPN acyltransferase (IAT), which is encoded by the penDE gene. In silico analysis of the P. chrysogenum genome revealed the presence of a gene, Pc13g09140, initially described as paralogue of the IAT-encoding penDE gene. We have termed this gene ial because it encodes a protein with high similarity to IAT (IAL for IAT-Like). We have conducted an investigation to characterize the ial gene and to determine the role of the IAL protein in the penicillin biosynthetic pathway.

Results
The IAL contains motifs characteristic of the IAT such as the processing site, but lacks the peroxisomal targeting sequence ARL. Null ial mutants and overexpressing strains indicated that IAL lacks acyltransferase (penicillin biosynthetic) and amidohydrolase (6-APA forming) activities in vivo. When the canonical ARL motif (leading to peroxisomal targeting) was added to the C-terminus of the IAL protein (IALARL) by site-directed mutagenesis, no penicillin biosynthetic activity was detected. Since the IAT is only active after an accurate self-processing of the preprotein into α and β subunits, self-processing of the IAL was tested in Escherichia coli. Overexpression experiments and SDS-PAGE analysis revealed that IAL is also self-processed in two subunits, but despite the correct processing, the enzyme remained inactive in vitro.

Conclusion
No activity related to the penicillin biosynthesis was detected for the IAL. Sequence comparison among the P. chrysogenum IAL, the A. nidulans IAL homologue and the IAT, revealed that the lack of enzyme activity seems to be due to an alteration of the essential Ser309 in the thioesterase active site. Homologues of the ial gene have been found in many other ascomycetes, including non-penicillin producers. Our data suggest that like in A. nidulans, the ial and penDE genes might have been formed from a single ancestral gene that became duplicated during evolution, although a separate evolutive origin for the ial and penDE genes, is also discussed.
DNA methylation-histone modification relationships across the desmin locus in human primary cells
Authors: Lindahl Allen Marianne , Koch Christoph M , Clelland Gayle K , Dunham Ian , Antoniou Michael 
Published: May 2009

Abstract

Background
We present here an extensive epigenetic analysis of a 500 kb region, which encompasses the human desmin gene (DES) and its 5' locus control region (LCR), the only muscle-specific transcriptional regulatory element of this type described to date. These data complement and extend Encyclopaedia of DNA Elements (ENCODE) studies on region ENr133. We analysed histone modifications and underlying DNA methylation patterns in physiologically relevant DES expressing (myoblast/myotube) and non-expressing (peripheral blood mononuclear) primary human cells.

Results
We found that in expressing myoblast/myotube but not peripheral blood mononuclear cell (PBMC) cultures, histone H4 acetylation displays a broadly distributed enrichment across a gene rich 200 kb region whereas H3 acetylation localizes at the transcriptional start site (TSS) of genes. We show that the DES LCR and TSS of DES are enriched with hyperacetylated domains of acetylated histone H3, with H3 lysine 4 di- and tri-methylation (H3K4me2 and me3) exhibiting a different distribution pattern across this locus. The CpG island that extends into the first intron of DES is methylation-free regardless of the gene's expression status and in non-expressing PBMCs is marked with histone H3 lysine 27 tri-methylation (H3K27me3).

Conclusion
Overall, our results constitute the first study correlating patterns of histone modifications and underlying DNA methylation of a muscle-specific LCR and its associated downstream gene region whilst additionally placing this within a much broader genomic context. Our results clearly show that there are distinct patterns of histone H3 and H4 acetylation and H3 methylation at the DES LCR, promoter and intragenic region. In addition, the presence of H3K27me3 at the DES methylation-free CpG only in non-expressing PBMCs may serve to silence this gene in non-muscle tissues. Generally, our work demonstrates the importance of using multiple, physiologically relevant tissue types that represent different expressing/non-expressing states when investigating epigenetic marks and that underlying DNA methylation status should be correlated with histone modification patterns when studying chromatin structure.
Hepatitis C virus NS4B carboxy terminal domain is a membrane binding domain
Authors: Liefhebber Jolanda MP , Brandt Bernd W , Broer Rene , Spaan Willy JM , van Leeuwen Hans C 
Published: May 2009

Abstract

Background
Hepatitis C virus (HCV) induces membrane rearrangements during replication. All HCV proteins are associated to membranes, pointing out the importance of membranes for HCV. Non structural protein 4B (NS4B) has been reported to induce cellular membrane alterations like the membranous web. Four transmembrane segments in the middle of the protein anchor NS4B to membranes. An amphipatic helix at the amino-terminus attaches to membranes as well. The carboxy-terminal domain (CTD) of NS4B is highly conserved in Hepaciviruses, though its function remains unknown.

Results
A cytosolic localization is predicted for the NS4B-CTD. However, using membrane floatation assays and immunofluorescence, we now show targeting of the NS4B-CTD to membranes. Furthermore, a profile-profile search, with an HCV NS4B-CTD multiple sequence alignment, indicates sequence similarity to the membrane binding domain of prokaryotic D-lactate dehydrogenase (d-LDH). The crystal structure of E. coli d-LDH suggests that the region similar to NS4B-CTD is located in the membrane binding domain (MBD) of d-LDH, implying analogy in membrane association. Targeting of d-LDH to membranes occurs via electrostatic interactions of positive residues on the outside of the protein with negative head groups of lipids. To verify that anchorage of d-LDH MBD and NS4B-CTD is analogous, NS4B-CTD mutants were designed to disrupt these electrostatic interactions. Membrane association was confirmed by swopping the membrane contacting helix of d-LDH with the corresponding domain of the 4B-CTD. Furthermore, the functionality of these residues was tested in the HCV replicon system.

Conclusion
Together these data show that NS4B-CTD is associated to membranes, similar to the prokaryotic d-LDH MBD, and is important for replication.
Properties of virion transactivator proteins encoded by primate cytomegaloviruses
Authors: Nicholson Iain P , Sutherland Jane S , Chaudry Tanya N , Blewett Earl L , Barry Peter A , Nicholl Mary Jane , Preston Chris M 
Published: May 2009

Abstract

Background
Human cytomegalovirus (HCMV) is a betaherpesvirus that causes severe disease in situations where the immune system is immature or compromised. HCMV immediate early (IE) gene expression is stimulated by the virion phosphoprotein pp71, encoded by open reading frame (ORF) UL82, and this transactivation activity is important for the efficient initiation of viral replication. It is currently recognized that pp71 acts to overcome cellular intrinsic defences that otherwise block viral IE gene expression, and that interactions of pp71 with the cell proteins Daxx and ATRX are important for this function. A further property of pp71 is the ability to enable prolonged gene expression from quiescent herpes simplex virus type 1 (HSV-1) genomes. Non-human primate cytomegaloviruses encode homologs of pp71, but there is currently no published information that addresses their effects on gene expression and modes of action.

Results
The UL82 homolog encoded by simian cytomegalovirus (SCMV), strain Colburn, was identified and cloned. This ORF, named S82, was cloned into an HSV-1 vector, as were those from baboon, rhesus monkey and chimpanzee cytomegaloviruses. The use of an HSV-1 vector enabled expression of the UL82 homologs in a range of cell types, and permitted investigation of their abilities to direct prolonged gene expression from quiescent genomes. The results show that all UL82 homologs activate gene expression, and that neither host cell type nor promoter target sequence has major effects on these activities. Surprisingly, the UL82 proteins specified by non-human primate cytomegaloviruses, unlike pp71, did not direct long term expression from quiescent HSV-1 genomes. In addition, significant differences were observed in the intranuclear localization of the UL82 homologs, and in their effects on Daxx. Strikingly, S82 mediated the release of Daxx from nuclear domain 10 substructures much more rapidly than pp71 or the other proteins tested. All UL82 homologs stimulated the early release of ATRX from nuclear domain 10.

Conclusion
All of the UL82 homolog proteins analysed activated gene expression, but surprising differences in other aspects of their properties were revealed. The results provide new information on early events in infection with cytomegaloviruses.