bluuebunny/crossref_metadata_2025_split huggingface dataset:
Wind-Driven Ageostrophic Transport in the North Equatorial Countercurrent of the Eastern Pacific at 95°W
Authors: Sprintall Janet , Kennan Sean , Kim Yoo Yin , Niiler Peter 
Published: June 2009

Abstract
Observations of horizontal velocity from two shipboard acoustic Doppler current profilers (ADCPs), as well as wind, temperature, and salinity observations from a cruise during June–July 2001, are used to compute a simplified mean meridional momentum balance of the North Equatorial Countercurrent (NECC) at 95°W. The terms that are retained in the momentum balance and derived using the measurements are the Coriolis and pressure gradient forces, and the vertical divergence of the turbulent stress. All terms were vertically integrated over the surface turbulent layer. The K-profile parameterization (KPP) prescribed Richardson number (Ri) is used to determine the depth of the turbulent boundary layer h at which the turbulent stress and its gradient vanish. At the time of the cruise, surface drifters and altimeter data show the flow structure of the NECC was complicated by the presence of tropical instability waves to the south and a strong Costa Rica Dome to the north. Nonetheless, a consistent, simplified momentum balance for the surface layer was achieved from the time mean of 19 days of repeat transects along 95°W with a 0.5° latitude resolution. The best agreement between the ageostrophic transport determined from the near-surface cruise measurements and the wind-derived Ekman transport was obtained for an Ri of 0.23 ± 0.05. The corresponding h ranges from ∼55 m at 4°N to ∼30 m within the NECC core (4.5°–6°N) and shoaling to just 15 m at 7°N. In general, the mean ageostrophic and Ekman transports decreased from south to north along the 95°W transect, although within the core of the NECC both transports were relatively strong and steady. This study underscores the importance of the southerly wind-driven eastward Ekman transport in the turbulent boundary layer before the NECC becomes fully developed later in the year through indirect forcing from the wind stress curl.
Characterizing Thermohaline Intrusions in the North Pacific Subtropical Frontal Zone
Authors: Shcherbina Andrey Y. , Gregg Michael C. , Alford Matthew H. , Harcourt Ramsey R. 
Published: June 2009

Abstract
A monthlong field survey in July 2007, focused on the North Pacific subtropical frontal zone (STFZ) near 30°N, 158°W, combined towed depth-cycling conductivity–temperature–depth (CTD) profiling with shipboard current observations. Measurements were used to investigate the distribution and structure of thermohaline intrusions. The study revealed that local extrema of vertical salinity profiles, often used as intrusion indicators, were only a subset of a wider class of distortions in thermohaline fields due to interleaving processes. A new method to investigate interleaving based on diapycnal spiciness curvature was used to describe an expanded class of laterally coherent intrusions. STFZ intrusions were characterized by their overall statistics and by a number of case studies. Thermohaline interleaving was particularly intense within 5 km of two partially compensated fronts, where intrusions with both positive and negative salinity anomalies were widespread. The vertical and cross-frontal scales of the intrusions were on the order of 10 m and 5 km, respectively. Though highly variable, the slopes of these features were typically intermediate between those of isopycnals and isohalines. Although the influence of double-diffusive processes sometime during the evolution of intrusions could not be excluded, the broad spectrum of the observed features suggests that any role of double diffusion was secondary.
Assimilation of AIRS Radiances Affected by Mid- to Low-Level Clouds
Authors: Pangaud Thomas , Fourrie Nadia , Guidard Vincent , Dahoui Mohamed , Rabier Florence 
Published: June 2009

Abstract
An approach to make use of Atmospheric Infrared Sounder (AIRS) cloud-affected infrared radiances has been developed at Météo-France in the context of the global numerical weather prediction model. The method is based on (i) the detection and the characterization of clouds by the CO2-slicing algorithm and (ii) the identification of clear–cloudy channels using the ECMWF cloud-detection scheme. Once a hypothetical cloud-affected pixel is detected by the CO2-slicing scheme, the cloud-top pressure and the effective cloud fraction are provided to the radiative transfer model simultaneously with other atmospheric variables to simulate cloud-affected radiances. Furthermore, the ECMWF scheme flags each channel of the pixel as clear or cloudy. In the current configuration of the assimilation scheme, channels affected by clouds whose cloud-top pressure ranges between 600 and 950 hPa are assimilated over sea in addition to clear channels. Results of assimilation experiments are presented. On average, 3.5% of additional pixels are assimilated over the globe but additional assimilated channels are much more numerous for mid- to high latitudes (10% of additional assimilated channels on average). Encouraging results are found in the quality of the analyses: background departures of AIRS observations are reduced, especially for surface channels, which are globally 4 times smaller, and the analysis better fits some conventional and satellite data. Global forecasts are slightly improved for the geopotential field. These improvements are significant up to the 72-h forecast range. Predictability improvements have been obtained for a case study: a low pressure system that affected the southeastern part of Italy in September 2006. The trajectory, intensity, and the whole development of the cyclogenesis are better predicted, whatever the forecast range, for this case study.
Planetary Waves, Cyclogenesis, and the Irregular Breakdown of Zonal Motion over the North Atlantic
Authors: Roebber Paul J. 
Published: June 2009

Abstract
Numerous observational and modeling studies have suggested the importance of cyclogenesis to the breakdown of the zonal flow and the maintenance of atmospheric blocks, whereas other studies have shown that low-frequency dynamics are sufficient to produce and maintain these patterns. Experiments with a simple model of the general circulation and empirical evidence obtained from reanalysis and cyclone tracking data are used to develop a conceptual understanding of this irregular response. The model’s results and observational data are consistent with the idea that the North Atlantic flow response to cyclone forcing is preconditioned by the state of the hemispheric circulation. A characteristic hemispheric flow configuration reminiscent of the shedding of a potential vorticity (PV) filament and tightening of the PV gradient is particularly responsive to cyclogenesis, with the likelihood of below 10th percentile North Atlantic zonal flow under these conditions increased by a factor of 2.37 for each cyclone event. A second characteristic pattern, reminiscent of the PV wave-breaking anticyclonic roll up, responds in an opposite way to cyclogenesis, with a decrease in the likelihood of below 10th percentile zonal flow by a factor of 0.67. This perspective is connected to the decades of research on blocking and opens an opportunity for the development of medium-range forecast model postprocessors that might provide probabilistic forecasts of North Atlantic flow transitions.
CORRIGENDUM: False Alarm Rate or False Alarm Ratio?
Authors: Barnes Lindsey R. , Schultz David M. , Gruntfest Eve C. , Hayden Mary H. , Benight Charles C. 
Published: June 2009

Abstract
Two items need to be clarified from an earlier work of the authors. The first is that the layout of the 2 × 2 contingency table was reversed from standard practice, with the titles of “observed event” and “forecast” transposed. The second is that FAR should have represented “false alarm ratio,” not “false alarm rate.” Unfortunately, the terminology used in the atmospheric sciences is confusing, with authors as early as 1965 having used the terminology differently from currently accepted practice. More recent studies are not much better. A survey of peer-reviewed articles published in American Meteorological Society journals between 2001 and 2007 found that, of 26 articles using those terms, 10 (38%) used them inconsistently with the currently accepted definitions. This article recommends that authors make explicit how their verification statistics are calculated in their manuscripts and consider using the terms probability of false detection and probability of false alarm instead of false alarm rate and false alarm ratio.
The prevalence of depression in hereditary spastic paraplegia
Authors: Vahter L. , Braschinsky M. , Haldre S. , Gross-Paju K. 
Published: June 2009

Objective: To evaluate the prevalence of depression and sensitivity and specificity of the single-item interview ‘Are you depressed?’ for people with hereditary spastic paraplegia in Estonia. Design: Single-item interview ‘Are you depressed?’ was used as a screening question for depression; all participants then completed the Beck Depression Inventory. Setting: People with hereditary spastic paraplegia identified from the epidemiological database who agreed to participate in the study. Main measures: Beck Depression Inventory, clinical interview. Results: The epidemiological database consisted of 59 patients with clinically confirmed diagnosis of hereditary spastic paraplegia. Forty-eight of these consented to participate in the study. The Beck Depression Inventory score was higher than cut-off point in 58% (28/48) and lower in 42% (20/48). Of the study group, 44% (21/48) had mild, 13% (6/48) moderate and one person revealed severe depression. There was a statistically significant correlation between Beck Depression Inventory score and level of mobility; no other significant correlations with other measures were detected. Of the participants, 54% (26/48) had subjective complaints about depression and answered ‘Yes’ to the single-item interview ‘Are you depressed?’. The sensitivity of the one-item interview in the hereditary spastic paraplegia group was 75% and specificity 75%. Conclusions: Our results show that mild depression is prevalent among people with hereditary spastic paraplegia. Although the single question may be helpful, it cannot be relied upon entirely when assessing a person for depression.
The Docking Technique for Medial Patellofemoral Ligament Reconstruction
Authors: Ahmad Christopher S. , Brown Gabriel D. , Stein Beth Shubin 
Published: June 2009

Background Current techniques of medial patellofemoral ligament (MPFL) reconstruction vary with respect to methods of fixation on the femur and the patella. This article presents the outcomes of a surgical technique for reconstruction of the MPFL that uses a soft tissue graft with interference screw fixation on the femur and a docking technique for fixation on the patella. Hypothesis Patients with patellar instability who are treated with the docking technique for MPFL reconstruction will have improvements in knee symptoms and function, with a high percentage achieving good to excellent results at early follow-up. Study Design Case series; Level of evidence, 4. Methods Twenty consecutive patients with patellar instability underwent reconstruction of the MPFL. Patients were evaluated preoperatively and postoperatively by physical and radiographic examination and subjectively with the IKDC (International Knee Documentation Committee), Tegner, Kujala, and Lysholm questionnaires. Nineteen patients underwent magnetic resonance imaging preoperatively. Results The average follow-up was 31 months (range, 24–39). No recurrent episodes of dislocation or subluxation were reported. A firm endpoint to lateral patellar translation was noted in all patients at most recent follow-up. The IKDC subjective knee evaluation score improved from 42 preoperatively to 82 postoperatively ( P< .001); Kujala, from 50 to 88 ( P< .001); Lysholm, from 50 to 89 ( P< .001); and Tegner, from 3.6 to 5.6 ( P< .001). Conclusion The docking technique for MPFL reconstruction is an effective surgical procedure for the treatment of patellar instability.
Early epigenetic changes and DNA damage do not predict clinical response in an overlapping schedule of 5-azacytidine and entinostat in patients with myeloid malignancies
Authors: Fandy Tamer E. , Herman James G. , Kerns Patrick , Jiemjit Anchalee , Sugar Elizabeth A. , Choi Si-Ho , Yang Allen S. , Aucott Timothy , Dauses Tianna , Odchimar-Reissig Rosalie , Licht Jonathan , McConnell Melanie J. , Nasrallah Chris , Kim Marianne K. H. , Zhang Weijia , Sun Yezou , Murgo Anthony , Espinoza-Delgado Igor , Oteiza Katharine , Owoeye Ibitayo , Silverman Lewis R. , Gore Steven D. , Carraway Hetty E. 
Published: June 2009

Abstract
Sequential administration of DNA methyltransferase (DNMT) inhibitors and histone deacetylase (HDAC) inhibitors has demonstrated clinical efficacy in patients with hematologic malignancies. However, the mechanism behind their clinical efficacy remains controversial. In this study, the methylation dynamics of 4 TSGs (p15INK4B, CDH-1, DAPK-1, and SOCS-1) were studied in sequential bone marrow samples from 30 patients with myelodysplastic syndrome (MDS) or acute myeloid leukemia (AML) who completed a minimum of 4 cycles of therapy with 5-azacytidine and entinostat. Reversal of promoter methylation after therapy was observed in both clinical responders and nonresponders across all genes. There was no association between clinical response and either baseline methylation or methylation reversal in the bone marrow or purified CD34+ population, nor was there an association with change in gene expression. Transient global hypomethylation was observed in samples after treatment but was not associated with clinical response. Induction of histone H3/H4 acetylation and the DNA damage–associated variant histone γ-H2AX was observed in peripheral blood samples across all dose cohorts. In conclusion, methylation reversal of candidate TSGs during cycle 1 of therapy was not predictive of clinical response to combination “epigenetic” therapy. This trial is registered with http://www.clinicaltrials.gov under NCT00101179.
Reintroduction of CEBPA in MN1-overexpressing hematopoietic cells prevents their hyperproliferation and restores myeloid differentiation
Authors: Kandilci Ayten , Grosveld Gerard C. 
Published: June 2009

Abstract
Forced expression of MN1 in primitive mouse hematopoietic cells causes acute myeloid leukemia and impairs all-trans retinoic acid-induced granulocytic differentiation. Here, we studied the effects of MN1 on myeloid differentiation and proliferation using primary human CD34+ hematopoietic cells, lineage-depleted mouse bone marrow cells, and bipotential (granulocytic/monocytic) human acute myeloid leukemia cell lines. We show that exogenous MN1 stimulated the growth of CD34+ cells, which was accompanied by enhanced survival and increased cell cycle traverse in cultures supporting progenitor cell growth. Forced MN1 expression impaired both granulocytic and monocytic differentiation in vitro in primary hematopoietic cells and acute myeloid leukemia cell lines. Endogenous MN1 expression was higher in human CD34+ cells compared with both primary and in vitro–differentiated monocytes and granulocytes. Microarray and real-time reverse-transcribed polymerase chain reaction analysis of MN1-overexpressing CD34+ cells showed down-regulation of CEBPA and its downstream target genes. Reintroduction of conditional and constitutive CEBPA overcame the effects of MN1 on myeloid differentiation and inhibited MN1-induced proliferation in vitro. These results indicate that down-regulation of CEBPA activity contributes to MN1-modulated proliferation and impaired myeloid differentiation of hematopoietic cells.
Editorial
Authors: Bodin Loys 
Published: June 2009

Abstract
The Institut National de la Recherche Agronomique (INRA) was honoured to welcome scientists from all over the world who attended the International Workshop on major Genes and QTL in Sheep and Goats. Approximately 100 participants from 16 countries were registered, contributing 52 oral or poster presentations.
A first session was dedicated to the tools available for identifying and localising major genes or QTL in these two species. Molecular techniques, marker panels, radiation hybrids, genome physical maps, and BAC libraries were presented along with genetic, comparative and cytogenetic maps. A second and largest session concerned different traits for which major genes or QTL have been found, i.e., ovulation and other reproduction traits, milk and meat characters, and resistance to disease and wool production. For each group, a guest's paper focused on one sub-trait gave the state of the art: the history, identification and localisation of sources of monogenic and oligogenic variability, genetic determinism (dominance, imprinting, ...), effects on the phenotype, physiological mechanisms implied, use in populations, etc. The third session was devoted to the strategies for the use of major genes and QTL in populations, while the last session covered future prospects.
A CD (available on request to bodin@toulouse.inra.fr) of the full proceedings was available, and participants invited to give a main paper also had the opportunity to submit it for publication in this special issue of GSE. Nine articles were jointly selected by the Editorial Board of the journal and by the Guest Editor.
Alveolar hypoxia, alveolar macrophages, and systemic inflammation
Authors: Chao Jie , Wood John G , Gonzalez Norberto C 
Published: June 2009

Abstract
Diseases featuring abnormally low alveolar PO2 are frequently accompanied by systemic effects. The common presence of an underlying inflammatory component suggests that inflammation may contribute to the pathogenesis of the systemic effects of alveolar hypoxia. While the role of alveolar macrophages in the immune and defense functions of the lung has been long known, recent evidence indicates that activation of alveolar macrophages causes inflammatory disturbances in the systemic microcirculation. The purpose of this review is to describe observations in experimental animals showing that alveolar macrophages initiate a systemic inflammatory response to alveolar hypoxia. Evidence obtained in intact animals and in primary cell cultures indicate that alveolar macrophages activated by hypoxia release a mediator(s) into the circulation. This mediator activates perivascular mast cells and initiates a widespread systemic inflammation. The inflammatory cascade includes activation of the local renin-angiotensin system and results in increased leukocyte-endothelial interactions in post-capillary venules, increased microvascular levels of reactive O2 species; and extravasation of albumin. Given the known extrapulmonary responses elicited by activation of alveolar macrophages, this novel phenomenon could contribute to some of the systemic effects of conditions featuring low alveolar PO2.
Modeling the role of p53 pulses in DNA damage- induced cell death decision
Authors: Sun Tingzhe , Chen Chun , Wu Yuanyuan , Zhang Shuai , Cui Jun , Shen Pingping 
Published: June 2009

AbstractBackgroundThe tumor suppressor p53 plays pivotal roles in tumorigenesis suppression. Although oscillations of p53 have been extensively studied, the mechanism of p53 pulses and their physiological roles in DNA damage response remain unclear.ResultsTo address these questions we presented an integrated model in which Ataxia-Telangiectasia Mutated (ATM) activation and p53 oscillation were incorporated with downstream apoptotic events, particularly the interplays between Bcl-2 family proteins. We first reproduced digital oscillation of p53 as the response of normal cells to DNA damage. Subsequent modeling in mutant cells showed that high basal DNA damage is a plausible cause for sustained p53 pulses observed in tumor cells. Further computational analyses indicated that p53-dependent PUMA accumulation and the PUMA-controlled Bax activation switch might play pivotal roles to count p53 pulses and thus decide the cell fate.ConclusionThe high levels of basal DNA damage are responsible for generating sustained pulses of p53 in the tumor cells. Meanwhile, the Bax activation switch can count p53 pulses through PUMA accumulation and transfer it into death signal. Our modeling provides a plausible mechanism about how cells generate and orchestrate p53 pulses to tip the balance between survival and death.
OrthoClusterDB: an online platform for synteny blocks
Authors: Ng Man-Ping , Vergara Ismael A , Frech Christian , Chen Qingkang , Zeng Xinghuo , Pei Jian , Chen Nansheng 
Published: June 2009

Abstract

Background
The recent availability of an expanding collection of genome sequences driven by technological advances has facilitated comparative genomics and in particular the identification of synteny among multiple genomes. However, the development of effective and easy-to-use methods for identifying such conserved gene clusters among multiple genomes–synteny blocks–as well as databases, which host synteny blocks from various groups of species (especially eukaryotes) and also allow users to run synteny-identification programs, lags behind.

Descriptions
OrthoClusterDB is a new online platform for the identification and visualization of synteny blocks. OrthoClusterDB consists of two key web pages: Run OrthoCluster and View Synteny. The Run OrthoCluster page serves as web front-end to OrthoCluster, a recently developed program for synteny block detection. Run OrthoCluster offers full control over the functionalities of OrthoCluster, such as specifying synteny block size, considering order and strandedness of genes within synteny blocks, including or excluding nested synteny blocks, handling one-to-many orthologous relationships, and comparing multiple genomes. In contrast, the View Synteny page gives access to perfect and imperfect synteny blocks precomputed for a large number of genomes, without the need for users to retrieve and format input data. Additionally, genes are cross-linked with public databases for effective browsing. For both Run OrthoCluster and View Synteny, identified synteny blocks can be browsed at the whole genome, chromosome, and individual gene level. OrthoClusterDB is freely accessible.

Conclusion
We have developed an online system for the identification and visualization of synteny blocks among multiple genomes. The system is freely available at http://genome.sfu.ca/orthoclusterdb/.
Generation and characterization of human insulin-releasing cell lines
Authors: Labriola Leticia , Peters Maria G , Krogh Karin , Stigliano Iván , Terra Letícia F , Buchanan Cecilia , Machado Marcel CC , Joffé Elisa Bal de Kier , Puricelli Lydia , Sogayar Mari C 
Published: June 2009

Abstract

Background
The in vitro culture of insulinomas provides an attractive tool to study cell proliferation and insulin synthesis and secretion. However, only a few human beta cell lines have been described, with long-term passage resulting in loss of insulin secretion. Therefore, we set out to establish and characterize human insulin-releasing cell lines.

Results
We generated ex-vivo primary cultures from two independent human insulinomas and from a human nesidioblastosis, all of which were cultured up to passage number 20. All cell lines secreted human insulin and C-peptide. These cell lines expressed neuroendocrine and islets markers, confirming the expression profile found in the biopsies. Although all beta cell lineages survived an anchorage independent culture, none of them were able to invade an extracellular matrix substrate.

Conclusion
We have established three human insulin-releasing cell lines which maintain antigenic characteristics and insulin secretion profiles of the original tumors. These cell lines represent valuable tools for the study of molecular events underlying beta cell function and dysfunction.