bluuebunny/crossref_metadata_2025_split huggingface dataset:
Baroclinic Flow around Planetary Islands in a Double Gyre: A Mechanism for Cross-Gyre Flow
Authors: Pedlosky Joseph 
Published: January 2010

Abstract
A quasigeostrophic, two-layer model is used to study the baroclinic circulation around a thin, meridionally elongated island. The flow is driven by either buoyancy forcing or wind stress, each of whose structure would produce an antisymmetric double-gyre flow. The ocean bottom is flat. When the island partially straddles the intergyre boundary, fluid from one gyre is forced to flow into the other. The amount of the intergyre flow depends on the island constant, that is, the value of the geostrophic streamfunction on the island in each layer. That constant is calculated in a manner similar to earlier studies and is determined by the average, along the meridional length of the island, of the interior Sverdrup solution just to the east of the island.
Explicit solutions are given for both buoyancy and wind-driven flows. The presence of an island of nonzero width requires the determination of the baroclinic streamfunction on the basin’s eastern boundary. The value of the boundary term is proportional to the island’s area. This adds a generally small additional baroclinic intergyre flow. In all cases, the intergyre flow produced by the island is not related to topographic steering of the flow but rather the pressure anomaly on the island as manifested by the barotropic and baroclinic island constants. The vertical structure of the flow around the island is a function of the parameterization of the vertical mixing in the problem and, in particular, the degree to which long baroclinic Rossby waves can traverse the basin before becoming thermally damped.
A New Three-Dimensional Visualization System for Combining Aircraft and Radar Data and Its Application to RICO Observations
Authors: Arthur Dan K. , Lasher-Trapp Sonia , Abdel-Haleem Ayman , Klosterman Nicholas , Ebert David S. 
Published: January 2010

Abstract
The analysis of diverse datasets from meteorological field campaigns often involves the use of separate 1D or combined 2D plots from various applications, making the determination of spatial and temporal relationships and correlations among these data, and the overall synthesis of information, extremely challenging. Presented here is a new 3D visualization tool, the Aircraft and Radar Data Collocation and Analysis in 3D (ARCA3D), that can combine data collected from different sources and at different scales, utilizing advanced visualization and user interface techniques, which allows for easier comparison and synthesis of such disparate data. The 3D tool is demonstrated with aircraft-based microphysical probe data and ground-based dual-polarization radar data all collected during the Rain in Cumulus over the Ocean (RICO) field campaign. The 3D volumes of radar data can be interactively selected and quantitatively probed, while aircraft-measured variables can be viewed along the aircraft track plotted within the 3D radar volumes or plotted as time series within regions of interest relative to the radar echoes. The greatest benefits of the new software, the 3D viewing of large radar and aircraft datasets with user-driven controls, are difficult to communicate here in a static, 2D written medium, but the application of the tool toward a research problem is presented to elucidate the impacts of these benefits. The ARCA3D software is used to investigate the possible role of giant aerosol particles in the development of precipitation in trade wind cumuli. The temporal trends in the spatial location of the maximum differential reflectivity echoes within the clouds are examined with respect to the ambient giant aerosol number concentration and the measured cloud-base droplet number concentrations on 10 days. The results indicate that in trade wind cumuli of sufficient depth, giant aerosol may determine the original location of the earliest differential reflectivity maximum echo, and thus the first raindrops when present in higher number concentrations. However, when the giant aerosol are less plentiful, the number of cloud droplets activated above the cloud base may also play a role in determining the location of the earliest maximum differential reflectivity echo, and thus the earliest raindrops, in these trade wind cumuli.
Calibration, Response, and Hysteresis in Deep-Sea Dissolved Oxygen Measurements
Authors: Edwards Bradley , Murphy David , Janzen Carol , Larson Nordeen 
Published: January 2010

Abstract
Accurately measuring the dissolved oxygen concentration in the ocean has been the subject of considerable research. Traditionally, the calibration and correction of profiling oxygen measurements has centered on static, steady-state errors, leaving dynamic or time-dependent errors in the sensor response largely untreated. This study evaluates a reengineered Sea-Bird Electronics dissolved-oxygen Clark electrode (SBE 43) and demonstrates the characterization of sensor time response over oceanographic temperatures and pressures as well as treating a time-dependent, pressure-induced effect observed as hysteresis, most notably in deep-ocean oxygen profiles. The effects of temperature and pressure on sensor response are measured separately and then combined into an expression for evaluating an in situ time constant. The physics of the pressure-induced hysteresis in oxygen sensors are discussed and modeled for many individual sensors in several locations throughout the world’s oceans. This effort reduces the underlying uncertainty of Clark oxygen sensors to approximately 0.1% of the measured signal, which is equivalent to the accuracy of the chemical calibration standard.
Effect of Two-Way Air–Sea Coupling in High and Low Wind Speed Regimes
Authors: Chen Sue , Campbell Tim J. , Jin Hao , Gaberšek Saša , Hodur Richard M. , Martin Paul 
Published: January 2010

AbstractA recent advance in the Coupled Ocean–Atmosphere Mesoscale Prediction System (COAMPS) is described and used to study two-way air–sea coupling and its impact on two different weather scenarios. The first case examines the impact of a hurricane-induced cold ocean wake on simulated changes in the structure of Hurricane Katrina. The second case investigates the effect of wind- and current-induced island wakes and their impact on the local electromagnetic (EM) and acoustic propagation characteristics in the Southern California Bight region. In the Katrina case, both the atmosphere and ocean show a strong response from air–sea interaction. The model results show that wind-induced turbulent mixing, vertical advection, and horizontal advection are the three primary causes of the development of the trailing cold ocean wake. A distinct spatial separation is seen in these three primary forcing terms that are generating the bulk of the cooling in the ocean mixed layer. An asymmetric tropical cyclone structure change has been documented in detail from a more realistic, full physics, and tightly coupled model. These changes include a broadening of the eye, a reduced radius of hurricane-force wind, and a pronounced inner-core dry slot on the west side of the storm. In the island wake experiment, many finescale variations in the wind, current, and static stability structure resulting from the two-way interaction are described. These variations take the form of narrow vorticity and temperature anomalies that are found to reside in the ocean and atmosphere well downwind from the Channel Islands. Upwind differences in the lower-atmospheric wind and thermal structure also arise and are found to have a small impact on the lee-flow structure and EM characteristics of the southernmost Channel Islands.
Reevaluating the Role of the Saharan Air Layer in Atlantic Tropical Cyclogenesis and Evolution
Authors: Braun Scott A. 
Published: January 2010

Abstract
The existence of the Saharan air layer (SAL), a layer of warm, dry, dusty air frequently present over the tropical Atlantic Ocean, has long been appreciated. The nature of its impacts on hurricanes remains unclear, with some researchers arguing that the SAL amplifies hurricane development and with others arguing that it inhibits it. The potential negative impacts of the SAL include 1) vertical wind shear associated with the African easterly jet; 2) warm air aloft, which increases thermodynamic stability at the base of the SAL; and 3) dry air, which produces cold downdrafts. Multiple NASA satellite datasets and NCEP global analyses are used to characterize the SAL’s properties and evolution in relation to tropical cyclones and to evaluate these potential negative influences. The SAL is shown to occur in a large-scale environment that is already characteristically dry as a result of large-scale subsidence. Strong surface heating and deep dry convective mixing enhance the dryness at low levels (primarily below ∼700 hPa), but moisten the air at midlevels. Therefore, mid- to-upper-level dryness is not generally a defining characteristic of the SAL, but is instead often a signature of subsidence. The results further show that storms generally form on the southern side of the jet, where the background cyclonic vorticity is high. Based upon its depiction in NCEP Global Forecast System meteorological analyses, the jet often helps to form the northern side of the storms and is present to equal extents for both strengthening and weakening storms, suggesting that jet-induced vertical wind shear may not be a frequent negative influence. Warm SAL air is confined to regions north of the jet and generally does not impact the tropical cyclone precipitation south of the jet.
Composite analyses of the early stages of tropical cyclones occurring in association with the SAL support the inferences from the individual cases noted above. Furthermore, separate composites for strongly strengthening and for weakening storms show few substantial differences in the SAL characteristics between these two groups, suggesting that the SAL is not a determinant of whether a storm will intensify or weaken in the days after formation. Key differences between these cases are found mainly at upper levels where the flow over strengthening storms allows for an expansive outflow and produces little vertical shear, while for weakening storms, the shear is stronger and the outflow is significantly constrained.
Inhomogeneous Background Error Modeling and Estimation over Antarctica
Authors: Michel Yann , Auligné Thomas 
Published: January 2010

Abstract
The structure of the analysis increments in a variational data assimilation scheme is strongly driven by the formulation of the background error covariance matrix, especially in data-sparse areas such as the Antarctic region. The gridpoint background error modeling in this study makes use of regression-based balance operators between variables, empirical orthogonal function decomposition to define the vertical correlations, gridpoint variances, and high-order efficient recursive filters to impose horizontal correlations. A particularity is that the regression operators and the recursive filters have been made spatially inhomogeneous. The computation of the background error statistics is performed with the Weather Research and Forecast (WRF) model from a set of forecast differences. The mesoscale limited-area domains of interest cover Antarctica. Inhomogeneities of background errors are shown to be related to the particular orography and physics of the area. Differences seem particularly pronounced between ocean and land boundary layers.
Treatment of latent Mycobacterium tuberculosis infection in intravenous drug users co-infected with HIV
Authors: Sánchez Francesca , Balagué Montse , García de Olalla Patricia , López Colomés José L. , Martín Vicente , Guerrero Rafael , Marco Andrés , Caylà Joan A. 
Published: January 2010

Objective: This clinical trial, carried out among injection drug users and the HIV-infected with tuberculin skin test ≥ 5 mm, aimed to evaluate the compliance and tolerability of two preventive strategies against tuberculosis (TB). Methods: Study protocol prospectively compares adherence to nine months of daily therapy with isoniazid (9H) versus two months of daily therapy with rifampin plus pyrazinamide (2RZ) administered randomly. All patients were concurrently admitted to a methadone maintenance programme. To assess toxicity, liver function was monitored monthly. Results: From 305 assessable patients, those in 2RZ arm showed better adherence (84% vs. 59%, p < 0.0001). Results on liver toxicity did not show significant differences between 9H and 2RZ (4.5% vs. 6.9%; odds ratio = 1.58, 95% confidence interval = 0.42—7.24). Conclusion: 2RZ should be considered an option to prevent TB in selected groups of patients infected with HIV, such as injection drug users on methadone treatment.
Deletion of the p110β isoform of phosphoinositide 3-kinase in platelets reveals its central role in Akt activation and thrombus formation in vitro and in vivo
Authors: Martin Valérie , Guillermet-Guibert Julie , Chicanne Gaétan , Cabou Cendrine , Jandrot-Perrus Martine , Plantavid Monique , Vanhaesebroeck Bart , Payrastre Bernard , Gratacap Marie-Pierre 
Published: January 2010

Abstract
During platelet activation, phosphoinositide 3-kinases (PI3Ks) produce lipid second messengers participating in the regulation of functional responses. Here, we generated a megakaryocyte-restricted p110β null mouse model and demonstrated a critical role of PI3Kβ in platelet activation via an immunoreceptor tyrosine-based activation motif, the glyco-protein VI-Fc receptor γ-chain complex, and its contribution in response to G-protein–coupled receptors. Interestingly, the production of phosphatidylinositol 3,4,5-trisphosphate and the activation of protein kinase B/Akt were strongly inhibited in p110β null platelets stimulated either via immunoreceptor tyrosine-based activation motif or G-protein–coupled receptors. Functional studies showed an important delay in fibrin clot retraction and an almost complete inability of these platelets to adhere onto fibrinogen under flow condition, suggesting that PI3Kβ is also acting downstream of αIIbβ3. In vivo studies showed that these mice have a normal bleeding time and are not protected from acute pulmonary thromboembolism but are resistant to thrombosis after FeCl3 injury of the carotid, suggesting that PI3Kβ is a potential target for antithrombotic drugs.
TAK1 targeting by glucocorticoids determines JNK and IκB regulation in Toll-like receptor–stimulated macrophages
Authors: Bhattacharyya Sandip , Ratajczak Christine K. , Vogt Sherri K. , Kelley Crystal , Colonna Marco , Schreiber Robert D. , Muglia Louis J. 
Published: January 2010

AbstractGlucocorticoids potently attenuate the production of inflammatory mediators by macrophages, a primary effector of innate immunity. Activation of different macrophage Toll-like receptors (TLRs) by their respective ligands presents a powerful system by which to evaluate stimulus-dependent glucocorticoid effects in the same cell type. Here, we test the hypothesis that glucocorticoids, acting through the glucocorticoid receptor, modulate macrophage activation preferentially depending upon the TLR-selective ligand and TLR adapters. We established that 2 adapters, Trif, MyD88, or both, determine the ability of glucocorticoids to suppress inhibitor of κB (IκB) degradation or Janus kinase (JNK) activation. Moreover, the sensitivity of transforming growth factor β–activated kinase 1 (TAK1) activation to glucocorticoids determines these effects. These findings identify TAK1 as a novel target for glucocorticoids that integrates their anti-inflammatory action in innate immunity signaling pathways.
High BAALC expression predicts chemoresistance in adult B-precursor acute lymphoblastic leukemia
Authors: Kühnl Andrea , Gökbuget Nicola , Stroux Andrea , Burmeister Thomas , Neumann Martin , Heesch Sandra , Haferlach Torsten , Hoelzer Dieter , Hofmann Wolf-Karsten , Thiel Eckhard , Baldus Claudia D. 
Published: January 2010

AbstractOverexpression of BAALC is an adverse prognostic factor in adults with cytogenetically normal acute myeloid leukemia and T-cell acute lymphoblastic leukemia (ALL). Here, we analyzed the prognostic significance of BAALC in B-precursor ALL. BAALC MRNA expression was determined in 368 primary adult B-precursor ALL patients enrolled on the 06/99 and 07/03 GMALL trials. Patients were grouped into tertiles according to BAALC expression (T1-T3). Higher BAALC expression (T3 vs T2 vs T1) was associated with higher age (P < .001), a higher white blood cell count (P = .008), CD34 (P = .001), BCR-ABL (P < .001), and MLL-AF4 (P < .001). Higher BAALC expression predicted primary therapy resistance in the overall cohort (P = .002) and in the BCR-ABL− and MLL-AF4− subgroup (P = .01). In BCR-ABL− and MLL-AF4− patients, higher BAALC expression was associated with a shorter overall survival (OS; 5-year OS: T3, 38%; T2, 52%; T1, 70%; P = .004) and independently predicted OS in multivariate models (P = .03). Gene-expression profiling revealed an up-regulation of stem cell markers and genes involved in chemoresistance (TSPAN7 and LYN) in the high BAALC group. Thus, high BAALC expression is associated with an immature, chemoresistant leukemic phenotype and identifies patients with inferior OS. Determination of BAALC might contribute to risk assessment of molecularly undefined adult B-precursor ALL.
FOG1 requires NuRD to promote hematopoiesis and maintain lineage fidelity within the megakaryocytic-erythroid compartment
Authors: Gregory Gregory D. , Miccio Annarita , Bersenev Alexey , Wang Yuhuan , Hong Wei , Zhang Zhe , Poncz Mortimer , Tong Wei , Blobel Gerd A. 
Published: January 2010

AbstractNuclear factors regulate the development of complex tissues by promoting the formation of one cell lineage over another. The cofactor FOG1 interacts with transcription factors GATA1 and GATA2 to control erythroid and megakaryocyte (MK) differentiation. In contrast, FOG1 antagonizes the ability of GATA factors to promote mast cell (MC) development. Normal FOG1 function in late-stage erythroid cells and MK requires interaction with the chromatin remodeling complex NuRD. Here, we report that mice in which the FOG1/NuRD interaction is disrupted (Fogki/ki) produce MK-erythroid progenitors that give rise to significantly fewer and less mature MK and erythroid colonies in vitro while retaining multilineage capacity, capable of generating MCs and other myeloid lineage cells. Gene expression profiling of Fogki/ki MK-erythroid progenitors revealed inappropriate expression of several MC-specific genes. Strikingly, aberrant MC gene expression persisted in mature Fogki/ki MK and erythroid progeny. Using a GATA1-dependent committed erythroid cell line, select MC genes were found to be occupied by NuRD, suggesting a direct mechanism of repression. Together, these observations suggest that a simple heritable silencing mechanism is insufficient to permanently repress MC genes. Instead, the continuous presence of GATA1, FOG1, and NuRD is required to maintain lineage fidelity throughout MK-erythroid ontogeny.
Neogenin inhibits HJV secretion and regulates BMP-induced hepcidin expression and iron homeostasis
Authors: Lee Dae-Hoon , Zhou Li-Juan , Zhou Zheng , Xie Jian-Xin , Jung Ji-Ung , Liu Yu , Xi Cai-Xia , Mei Lin , Xiong Wen-Cheng 
Published: January 2010

Abstract
Neogenin, a deleted in colorectal cancer (DCC) family member, has been identified as a receptor for the neuronal axon guidance cues netrins and repulsive guidance molecules repulsive guidance molecules (RGM). RGMc, also called hemojuvelin (HJV), is essential for iron homeostasis. Here we provide evidence that neogenin plays a critical role in iron homeostasis by regulation of HJV secretion and bone morphogenetic protein (BMP) signaling. Livers of neogenin mutant mice exhibit iron overload, low levels of hepcidin, and reduced BMP signaling. Mutant hepatocytes in vitro show impaired BMP2 induction of Smad1/5/8 phosphorylation and hepcidin expression. Neogenin is expressed in liver cells in a reciprocal pattern to that of hepcidin, suggesting that neogenin functions in a cell nonautonomous manner. Further studies demonstrate that neogenin may stabilize HJV, a glycosylphosphatidylinositol-anchored protein that interacts with neogenin and suppresses its secretion. Taken together, our results lead the hypothesis that neogenin regulates iron homeostasis via inhibiting secretion of HJV, an inhibitor of BMP signaling, to enhance BMP signaling and hepcidin expression. These results reveal a novel mechanism underlying neogenin regulation of HJV-BMP signaling.
Haploinsufficiency of Apc leads to ineffective hematopoiesis
Authors: Wang Jianghong , Fernald Anthony A. , Anastasi John , Le Beau Michelle M. , Qian Zhijian 
Published: January 2010

Abstract
Loss of a whole chromosome 5 or a deletion of the long arm of chromosome 5, −5/del(5q), is a recurring abnormality in myeloid neoplasms. The APC gene is located at chromosome band 5q23, and is deleted in more than 95% of patients with a −5/del(5q), raising the question of whether haploinsufficiency of APC contributes to the development of myeloid neoplasms with loss of 5q. We show that conditional inactivation of a single allele of Apc in mice leads to the development of severe anemia with macrocytosis and monocytosis. Further characterization of the erythroid lineage revealed that erythropoiesis is blocked at the early stages of differentiation. The long-term hematopoietic stem cell (LT-HSC) and short-term HSC (ST-HSC) populations are expanded in Apc-heterozygous mice compared with the control littermates; however, the HSCs have a reduced capacity to regenerate hematopoiesis in vivo in the absence of a single allele of Apc. Apc heterozygous myeloid progenitor cells display an increased frequency of apoptosis, and decreased in vitro colony-forming capacity, recapitulating several characteristic features of myeloid neoplasms with a −5/del(5q). Our results indicate that haploinsufficiency of Apc impairs hematopoiesis, and raise the possibility that loss of function of APC contributes to the development of myelodysplasia.
BLAST-EXPLORER helps you building datasets for phylogenetic analysis
Authors: Dereeper Alexis , Audic Stephane , Claverie Jean-Michel , Blanc Guillaume 
Published: January 2010

Abstract

Background
The right sampling of homologous sequences for phylogenetic or molecular evolution analyses is a crucial step, the quality of which can have a significant impact on the final interpretation of the study. There is no single way for constructing datasets suitable for phylogenetic analysis, because this task intimately depends on the scientific question we want to address, Moreover, database mining softwares such as BLAST which are routinely used for searching homologous sequences are not specifically optimized for this task.

Results
To fill this gap, we designed BLAST-Explorer, an original and friendly web-based application that combines a BLAST search with a suite of tools that allows interactive, phylogenetic-oriented exploration of the BLAST results and flexible selection of homologous sequences among the BLAST hits. Once the selection of the BLAST hits is done using BLAST-Explorer, the corresponding sequence can be imported locally for external analysis or passed to the phylogenetic tree reconstruction pipelines available on the Phylogeny.fr platform.

Conclusions
BLAST-Explorer provides a simple, intuitive and interactive graphical representation of the BLAST results and allows selection and retrieving of the BLAST hit sequences based a wide range of criterions. Although BLAST-Explorer primarily aims at helping the construction of sequence datasets for further phylogenetic study, it can also be used as a standard BLAST server with enriched output. BLAST-Explorer is available at http://www.phylogeny.fr