bluuebunny/crossref_metadata_2025_split huggingface dataset:
Atmospheric Circulation Regimes: Can Cluster Analysis Provide the Number?
Authors: Christiansen Bo 
Published: May 2007

AbstractThe existence of multiple regimes in the extratropical tropospheric circulation is a hypothesis of theoretical importance with potential practical consequences. It is also a controversial hypothesis, and an abundance of conflicting results regarding both the existence and the number of regimes can be found in the literature.Studies of atmospheric regime behavior are often based on clustering methods such as k-means and mixture models. In the basic implementation of these methods the number of clusters has to be specified a priori and “How many clusters?” is a highly nontrivial question. For the mixture model a procedure to assess the number of clusters by cross validation has recently been introduced. For the k-means model a Monte Carlo test is introduced that compares the clustering of the original data with the clustering of Gaussian distributed surrogate data. The robustness of these methods and their ability to produce the right number of clusters is critically assessed. The study is based on both idealized data and atmospheric data.It is shown that applying the clustering methods to the Northern Hemisphere winter tropospheric geopotential heights gives conflicting and fragile results. In particular the number of clusters depends both on the clustering algorithm and on the period considered. Furthermore, the clustering methods find multiple clusters when applied to data similar to the atmospheric data but drawn from a unimodal, skewed distribution.It is also shown that both clustering methods report multiple clusters for idealized data drawn from distributions that are skewed or platykurtic but otherwise smooth and without bumps or shoulders. In these cases the number of clusters found depends on the sample size. In particular, for the mixture model the number of clusters increases without bounds with increasing sample size.It is concluded that in the atmospheric dataset studied the clustering methods provide only weak evidence for multiple regimes although the data is non-Gaussian with high statistical significance. It is also concluded that statistical models with basically unknown properties should be approached with utmost care or avoided completely.
Rectification of ENSO Variability by Interdecadal Changes in the Equatorial Background Mean State in a CGCM Simulation
Authors: Dewitte Boris , Yeh Sang-Wook , Moon Byung-Kwon , Cibot Carole , Terray Laurent 
Published: May 2007

Abstract
The link between the changes in equatorial background stratification and El Niño–Southern Oscillation (ENSO) modulation is investigated using a simulation from a 260-yr-long coupled general circulation model (CGCM). The work focuses on the role of nonlinearities associated with equatorial wave dynamics. As a first step, the low-frequency change in mean stratification is diagnosed and documented from the shallow-water parameters derived from a vertical mode decomposition of the CGCM. The parameters vary differently according to the baroclinic mode order, which may explain why a flattening thermocline does not necessarily lead to reduced ENSO activity. Estimations of baroclinic mode contributions to zonal current anomalies indicate that the decadal variability projects differently for the baroclinic modes as compared to the interannual variability. In particular, the high-order modes associated with decadal variability have a more pronounced signature in the western Pacific, whereas that associated with interannual variability (i.e., ENSO) shows more energy in the eastern Pacific.
In the light of the results of the CGCM vertical mode decomposition, an intermediate coupled model (ICM) is used to test whether the nonlinearities associated with the changes in the baroclinic mode energy distribution can lead to coherent ENSO modulation. The results indicate that rectification of the interannual variability (ENSO time scales) by the interdecadal variability associated with changes in the oceanic mean states takes place in the ICM. The rectified effect results mostly in an increased variability and skewness of the zonal advection, which tends to produce a zonal seesaw of the sea surface temperature anomaly. A tropical mechanism for producing ENSO modulation is then proposed that reconciles both the rectified effect resulting from nonlinearities associated with equatorial wave dynamics and the tropical decadal mode of thermocline depth arising from Ekman-pumping anomalies located in the central South Pacific.
Modeling the Barrier-Layer Formation in the Southeastern Arabian Sea*
Authors: Durand F. , Shankar D. , de Boyer Montégut C. , Shenoi S. S. C. , Blanke B. , Madec G. 
Published: May 2007

AbstractThe effect of salinity on the formation of the barrier layer (BL) in the southeastern Arabian Sea (SEAS) is investigated using an ocean general circulation model. In accordance with previous studies, the runoff distribution and the India–Sri Lanka passage have a strong impact on the realism of the salinity simulated in the area at seasonal time scales. The model simulates a BL pattern in fairly good agreement with available observations. Eulerian and Lagrangian approaches show that the BL is formed by two complementary processes, the arrival of low-salinity surface waters that are cooled en route to the SEAS and downwelling of waters mostly local to the SEAS in the subsurface layers. The surface waters are partly of Bay of Bengal origin and are partly from the SEAS, but are cooled east and south of Sri Lanka in the model. That the downwelled subsurface waters are warm and are not cooled leads to temperature inversions in the BL. The main forcing for this appears to be remotely forced planetary waves.
What Drives the Seasonal Onset and Decay of the Western Hemisphere Warm Pool?
Authors: Lee S-K. , Enfield D. B. , Wang C. 
Published: May 2007

Abstract
The annual heat budget of the Western Hemisphere warm pool (WHWP) is explored using the output of an ocean general circulation model (OGCM) simulation. According to the analysis, the WHWP cannot be considered as a monolithic whole with a single set of dominating processes that explain its behavior. The three regions considered, namely the eastern north Pacific (ENP), the Gulf of Mexico (GoM), and the Caribbean Sea (CBN), are each unique in terms of the atmospheric and oceanic processes that dominate the corresponding heat budgets. In the ENP region, clear-sky shortwave radiation flux is responsible for the growth of the warm pool in boreal spring, while increased cloud cover in boreal summer and associated reduction in solar radiation play a crucial role for the ENP warm pool’s demise. Ocean upwelling in the Costa Rica Dome connected to surrounding areas by horizontal advection offers a persistent yearlong cooling mechanism. Over the Atlantic, the clear-sky radiation flux that increases monotonically from December to May and decreases later is largely responsible for the onset and decay of the Atlantic-side warm pool in boreal summer and fall. The CBN region is affected by upwelling and horizontal advective cooling within and away from the coastal upwelling zone off northern South America during the onset and peak phases, thus slowing down the warm pool’s development, but no evidence was found that advective heat flux divergence is important in the GoM region. Turbulent mixing is also an important cooling mechanism in the annual cycle of the WHWP, and the vertical shear at the warm pool base helps to sustain the turbulent mixing. Common to all three WHWP regions is the reduction of wind speed at the peak phase, suggestive of a convection–evaporation feedback known to be important in the Indo-Pacific warm pool dynamics.
The Sensitivity of the Rate of Transient Climate Change to Ocean Physics Perturbations
Authors: Collins M. , Brierley C. M. , MacVean M. , Booth B. B. B. , Harris G. R. 
Published: May 2007

Abstract
“Perturbed physics” ensembles of Hadley Centre climate models have recently been used to quantify uncertainties in atmospheric and surface climate feedbacks under enhanced levels of CO2, and to produce probabilistic estimates of the magnitude of equilibrium climate change. The rate of time-dependent climate change is determined both by the strength of atmosphere–surface climate feedbacks and by the strength of processes that remove heat from the surface to the deep ocean. Here a first small ensemble of coupled atmosphere–ocean climate model experiments in which the parameters that control three key ocean physical processes are perturbed is described. It is found that the perturbations have little impact on the rate of ocean heat uptake, and thus have little impact on the time-dependent rate of global warming. Under the idealized scenario of 1% yr−1 compounded CO2 increase, the spread in the transient climate response is of the order of a few tenths of a degree, in contrast to the spread of order of 1° caused by perturbing atmospheric model parameters.
Testing the Fixed Anvil Temperature Hypothesis in a Cloud-Resolving Model
Authors: Kuang Zhiming , Hartmann Dennis L. 
Published: May 2007

Abstract
Using cloud-resolving simulations of tropical radiative–convective equilibrium, it is shown that the anvil temperature changes by less than 0.5 K with a 2-K change in SST, lending support to the fixed anvil temperature (FAT) hypothesis. The results suggest that for plausible ozone profiles, a decrease in the air’s emission capability instead of ozone heating shall remain the control on the detrainment level, and the FAT hypothesis should hold. The anvil temperature also remains unchanged with other changes in the system such as the doubled CO2 mixing ratio, doubled stratospheric water vapor concentration, and dynamical cooling due to the Brewer–Dobson circulations. The results are robust when a different microphysics scheme is used.
Local versus Tropical Diabatic Heating and the Winter North Atlantic Oscillation
Authors: Greatbatch Richard J. , Jung Thomas 
Published: May 2007

Abstract
In this paper, a version of the European Centre for Medium-Range Weather Forecasts (ECMWF) operational model is used to (i) diagnose the diabatic heating associated with the winter North Atlantic Oscillation (NAO) and (ii) assess the role of this heating in the dynamics of the NAO in the model. Over the North Atlantic sector, the NAO-related diabatic heating is dominated above the planetary boundary layer by the latent heat release associated with precipitation, and within the boundary layer by vertical diffusion associated with sensible heat flux from the ocean. An association between La Niña–El Niño–type conditions in the tropical Pacific and the positive/negative NAO is found in model runs using initial conditions and sea surface temperature (SST) lower boundary conditions from the period 1982–2001, but not in a companion set of model runs for the period 1962–81. Model experiments are then described in which the NAO-related diabatic heating diagnosed from the 1982–2001 control run is applied as a constant forcing in the model temperature equation using both 1982–2001 and 1962–81 model setups. To assess the local feedback from the diabatic heating, the specified forcing is first restricted to the North Atlantic sector alone. In this case, the model response (in an ensemble mean sense) is suggestive of a weak negative feedback, but exhibits more baroclinic structure and has its centers of action shifted compared to those of the NAO. On the other hand, forcing with only the tropical Pacific part of the diabatic heating leads to a robust model response in both the 1982–2001 and 1962–81 model setups. The model response projects on to the NAO with the same sign as that used to diagnose the forcing, arguing that the link between the tropical Pacific and the NAO is real in the 1982–2001 control run. The missing link in the corresponding run for 1962–81 is a result of a change in the tropical forcing between the two periods, and not the extratropical flow regime.
Differences in Atmospheric Circulation between the Development of Weak and Strong Warm Events in the Southern Oscillation
Authors: Stephens David J. , Meuleners Michael J. , van Loon Harry , Lamond Malcolm H. , Telcik Nicola P. 
Published: May 2007

AbstractIn this study temporal and spatial aspects of El Niño (warm event) development are explored by comparing composite sequences of sea level pressure (SLP), surface wind, and sea surface temperature (SST) anomalies leading into strong and weak events. El Niño strength is found to be related to the magnitude and spatial extent of large-scale SLP anomalies that move in a low-frequency mode. In association with this, it is also intricately linked to the amplitude and wavelength of the Rossby waves in the southern midlatitudes. The primary signature of the Southern Oscillation is a more pronounced standing wave of pressure anomalies between southeastern Australia and the central South Pacific leading into stronger events. A strong reversal in the strength of the annual cycle between these two regions causes a stronger (weaker) SLP gradient that drives southwesterly (northwesterly) wind stress forcing toward (away from) the western equatorial Pacific in austral winter–spring of year 0 (−1). Thus, pressure variations in the southwest Pacific preconditions the equatorial environment to a particular phase of ENSO and establishes the setting for greater tropical–extratropical interactions to occur in stronger events.Maximum warming in the Niño-3 region occurs between April and July (0) when a strong South Pacific trough most influences the trade winds at both ends of the Pacific. Cool SST anomalies that form to the east of high pressure anomalies over Indo–Australia assist an eastward propogation of high pressure into the Pacific midlatitudes and the demise of El Niño. Strong events have a more pronounced eastward propogation of SST and SLP anomalies and a much more noticeable enhancement of winter hemisphere Rossby waves from May–July (−1) to November–January (+1). Weak events require an enhanced South Pacific trough to develop but have much less support from the North Pacific. They also appear more variable in their development and more difficult to predict with lead time.
Farnesyl transferase inhibitor resistance probed by target mutagenesis
Authors: Raz Tal , Nardi Valentina , Azam Mohammad , Cortes Jorge , Daley George Q. 
Published: May 2007

AbstractMutation in the target oncoprotein is a common mechanism of resistance to tyrosine kinase inhibitors, as exemplified by the many BCR/ABL mutations that thwart imatinib activity in patients with chronic myelogenous leukemia. It remains unclear whether normal cellular protein targets of chemotherapeutics will evolve drug resistance via mutation to a similar extent. We conducted an in vitro screen for resistance to lonafarnib, a farnesyl protein transferase inhibitor that blocks prenylation of a number of proteins important in cell proliferation, and identified 9 mutations clustering around the lonafarnib binding site. In patients treated with a combination of imatinib and lonafarnib, we identified farnesyl protein transferase mutations in residues identified in our screen. Substitutions at Y361 were found in patients prior to treatment initiation, suggesting that these mutants might confer a proliferative advantage to leukemia cells, which we were able to confirm in cell culture. In vitro mutagenesis of normal cellular enzymes can be exploited to identify mutations that confer chemotherapy resistance to novel agents.
Targeted cancer therapy with a novel low-dose rate α-emitting radioimmunoconjugate
Authors: Dahle Jostein , Borrebæk Jørgen , Jonasdottir Thora J. , Hjelmerud Anne Kristine , Melhus Katrine B. , Bruland Øyvind S. , Press Oliver W. , Larsen Roy H. 
Published: May 2007

Abstractα-emitting radionuclides are highly cytotoxic and are of considerable interest in the treatment of cancer. A particularly interesting approach is in radioimmunotherapy. However, α-emitting antibody conjugates have been difficult to exploit clinically due to the short half-life of the radionuclides, low production capability, or limited source materials. We have developed a novel technology based on the low-dose rate α-particle–emitting nuclide 227Th, exemplified here using the monoclonal antibody rituximab. In vitro, this radioimmunoconjugate killed lymphoma cells at Becquerel per milliliter (Bq/mL) levels. A single injection of 227Th-rituximab induced complete tumor regression in up to 60% of nude mice bearing macroscopic (32-256 mm3) human B-lymphoma xenografts at Becquerel per gram (Bq/g) levels without apparent toxicity. Therapy with 227Th-rituximab was significantly more effective than the control radioimmunoconjugate 227Th-trastuzumab and the standard β-emitting radioimmunoconjugate for CD20+ lymphoma90Y-tiuxetan-ibritumomab. Thorium-227 based constructs may provide a novel approach for targeted therapy against a wide variety of cancers.
Activity of vincristine, L-ASP, and dexamethasone against acute lymphoblastic leukemia is enhanced by the BH3-mimetic ABT-737 in vitro and in vivo
Authors: Kang Min H. , Kang Yun Hee , Szymanska Barbara , Wilczynska-Kalak Urszula , Sheard Michael A. , Harned Theresa M. , Lock Richard B. , Reynolds C. Patrick 
Published: May 2007

AbstractDefects in apoptosis signaling contribute to poor outcome in pediatric acute lymphoblastic leukemia (ALL), and overexpression of antiapoptotic Bcl-2 (Bcl-2 and Bcl-XL) family proteins has been observed in ALL. ABT-737 is a small-molecule BH3-mimetic that inhibits the antiapoptotic Bcl-2 family proteins. We evaluated the cytotoxicity of ABT-737 in combination with vincristine, dexamethasone, and L-asparaginase (VXL) in 7 ALL cell lines. Multilog synergistic cytotoxicity was observed in all 7 cell lines with ABT-737 plus L-asparaginase or vincristine, and in 5 of 7 cell lines with ABT-737 plus dexamethasone or VXL. In leukemia cells, but not in normal lymphocytes, ABT-737 plus L-asparaginase induced greater mitochondrial depolarization (JC-1 staining); mitochondrial cytochrome c release; activation of Bax, Bid, and caspases (immunoblotting); and eventually apoptosis (annexin V staining) than did either drug alone. In mouse xenografts derived from patients with ALL at diagnosis (ALL-7) or at relapse (ALL-19), event-free survival (EFS) was significantly enhanced with ABT-737 plus VXL relative to VXL or ABT-737 alone (P ≤ .02). Thus, ABT-737 synergistically enhanced VXL cytotoxicity in ALL cell lines via a mitochondrial death pathway and enhanced EFS in VXL-treated mice bearing ALL xenografts. Combining VXL with a BH3-mimetic warrants clinical investigation in ALL at relapse and potentially in chemotherapy-resistant ALL subgroups.
Dynamics of adipogenic promoter DNA methylation during clonal culture of human adipose stem cells to senescence
Authors: Noer Agate , Boquest Andrew C , Collas Philippe 
Published: May 2007

Abstract

Background
Potential therapeutic use of mesenchymal stem cells (MSCs) is likely to require large-scale in vitro expansion of the cells before transplantation. MSCs from adipose tissue can be cultured extensively until senescence. However, little is known on the differentiation potential of adipose stem cells (ASCs) upon extended culture and on associated epigenetic alterations. We examined the adipogenic differentiation potential of clones of human ASCs in early passage culture and upon senescence, and determined whether senescence was associated with changes in adipogenic promoter DNA methylation.

Results
ASC clones cultured to senescence display reduced adipogenic differentiation capacity in vitro, on the basis of limited lipogenesis and reduced transcriptional upregulation of FABP4 and LPL, two adipogenic genes, while LEP and PPARG2 transcription remains unaffected. In undifferentiated senescent cells, PPARG2 and LPL expression is unaltered, whereas LEP and FABP4 transcript levels are increased but not in all clones. Bisulfite sequencing analysis of DNA methylation reveals overall relative stability of LEP, PPARG2, FABP4 and LPL promoter CpG methylation during senescence and upon differentiation. Mosaicism in methylation profiles is maintained between and within ASC clones, and any CpG-specific methylation change detected does not necessarily relate to differentiation potential. One exception to this contention is CpG No. 21 in the LEP promoter, whose senescence-related methylation may impair upregulation of the gene upon adipogenic stimulation.

Conclusion
Senescent ASCs display reduced in vitro differentiation ability and transcriptional activation of adipogenic genes upon differentiation induction. These restrictions, however, cannot in general be attributed to specific changes in DNA methylation at adipogenic promoters. There also seems to be a correlation between CpGs that are hypomethylated and important transcription factor binding sites.
PCR-based landmark unique gene (PLUG) markers effectively assign homoeologous wheat genes to A, B and D genomes
Authors: Ishikawa Goro , Yonemaru Junichi , Saito Mika , Nakamura Toshiki 
Published: May 2007

AbstractBackgroundEST-PCR markers normally represent specific products from target genes, and are therefore effective tools for genetic analysis. However, because wheat is an allohexaploid plant, PCR products derived from homoeologous genes are often simultaneously amplified. Such products may be easier to differentiate if they include intron sequences, which are more polymorphic than exon sequences. However, genomic sequence data for wheat are limited; therefore it is difficult to predict the location of introns. By using the similarities in gene structures between rice and wheat, we developed a system called PLUG (PCR-based Landmark Unique Gene) to design primers so that PCR products include intron sequences. We then investigated whether products amplified using such primers could serve as markers able to distinguish multiple products derived from homoeologous genes.ResultsThe PLUG system consists of the following steps: (1) Single-copy rice genes (Landmark Unique Gene loci; LUGs) exhibiting high degrees of homology to wheat UniGene sequences are extracted; (2) Alignment analysis is carried out using the LUGs and wheat UniGene sequences to predict exon-exon junctions, and LUGs which can be used to design wheat primers flanking introns (TaEST-LUGs) are extracted; and (3) Primers are designed in an interactive manner. From a total of 4,312 TaEST-LUGs, 24 loci were randomly selected and used to design primers. With all of these primer sets, we obtained specific, intron-containing products from the target genes. These markers were assigned to chromosomes using wheat nullisomic-tetrasomic lines. By PCR-RFLP analysis using agarose gel electrophoresis, 19 of the 24 markers were located on at least one chromosome.ConclusionIn the development of wheat EST-PCR markers capable of efficiently sorting products derived from homoeologous genes, it is important to design primers able to amplify products that include intron sequences with insertion/deletion polymorphisms. Using the PLUG system, wheat EST sequences that can be used for marker development are selected based on comparative genomics with rice, and then primer sets flanking intron sequences are prepared in an interactive, semi-automatic manner. Hence, the PLUG system is an effective tool for large-scale marker development.