bluuebunny/crossref_metadata_2025_split huggingface dataset:
Methane in the northern Black Sea: characterization of its geomorphological and geological environments
Authors: Starostenko V. I. , Rusakov O. M. , Shnyukov E. F. , Kobolev V. P. , Kutas R. I. 
Published: September 2010

Abstract
Based on hydro-acoustic and geophysical observations, this paper presents an analysis of geomorphological and geological settings of gas methane occurrence on the NW shelf and upper continental slope, in the Sorokin trough and on the Kerch-Taman offshore, in the Black Sea. Gases are associated with seeps, mud volcanoes and gas hydrates. Evidence is given for the thermogenic nature of methane. The gas methane is of mostly abiogenic origin. Small gas releases may be produced by the decomposition of Quaternary organic material near the sea floor through the action of bacteria or biodegradation of redeposited thermogenic hydrocarbons. The origin of carbonate formations is related to degassing sedimentary layers. There is a possible role for deep faults in transporting gas to the sea floor. The gas hydrate stability zone in the Black Sea lies at minimum water depth of 600–650 m with its thickness up to 500 m.
Cretaceous–Neogene tectonic evolution of the northern margin of the Black Sea from seismic reflection data and tectonic subsidence analysis
Authors: Khriachtchevskaia O. , Stovba S. , Stephenson R. 
Published: September 2010

Abstract

Three fundamental stages of the Cretaceous–Neogene tectonic evolution of the Odessa Shelf and Azov Sea (northern margins of western and eastern Black Sea basins, respectively) have been documented from the analysis of reinterpreted regional seismic profiling and one-dimensional (1-D) subsidence analysis of 49 wells, for which the stratigraphic interpretation was recently revised. (1) An initial active rifting stage began within the Early Cretaceous (not later than Aptian–Albian times) and continued until the end of the Santonian in the Late Cretaceous (
c
. 128–83 Ma). A system of half-grabens with mainly south-dipping normal faults developed on the Odessa Shelf at this time. The most profound faulting, accompanied by volcanic activity, occurred in the NE–SW orientated Karkinit-Gubkin rift basin at the boundary between the Eastern European and Scythian platforms. The footwalls of half-grabens were exposed above sea level and subject to erosion at this time. Active extensional processes affected the western part of Azov Sea and, while the onset and cessation of these cannot be tightly constrained, they are compatible with the well constrained results from the Odessa Shelf. (2) The second tectonic stage is one of passive post-rift thermal subsidence that lasted from the Campanian (Late Cretaceous) until the end of the Middle Eocene (83–38.6 Ma). (3) The third stage of basin evolution is one of inversion tectonics in a compressional setting. Discrete inversion events occurred at the end of the Middle Eocene, during the Late Eocene, during the Early Miocene and at Middle Miocene times (
c
. 38.6 Ma,
c
. 35.4 Ma,
c
. 16.3 Ma,
c
. 10.4 Ma, respectively) and typical inversion structures developed on the Odessa Shelf, some parts of which were uplifted and significantly eroded (down to the Lower Cretaceous succession). The southern part of the Azov Sea, opening into the northernmost eastern Black Sea basin, subsided rapidly during this time; thereafter, until the Quaternary, rapid subsidence was limited to its southeastern part, which was incorporated into the Indolo-Kuban foreland basin of the Greater Caucasus orogen.
The byzantine empire in the intercloud
Authors: Vukolić Marko 
Published: September 2010

The relevance of Byzantine fault tolerance in the context of cloud computing has been questioned [3]. While arguments against Byzantine fault tolerance seemingly makes sense in the context of a single cloud, i.e., a large-scale cloud infrastructure that resides under control of a single, typically commercial provider, these arguments are less obvious in a broader context of the Intercloud, i.e., a cloud of multiple, independent clouds.
In this paper, we start from commonly acknowledged issues that impede the adoption of Byzantine fault tolerance within a single cloud, and argue that many of these issues fade when Byzantine fault tolerance in the Intercloud is considered.
A Comparison of PAM50 Intrinsic Subtyping with Immunohistochemistry and Clinical Prognostic Factors in Tamoxifen-Treated Estrogen Receptor–Positive Breast Cancer
Authors: Nielsen Torsten O. , Parker Joel S. , Leung Samuel , Voduc David , Ebbert Mark , Vickery Tammi , Davies Sherri R. , Snider Jacqueline , Stijleman Inge J. , Reed Jerry , Cheang Maggie C.U. , Mardis Elaine R. , Perou Charles M. , Bernard Philip S. , Ellis Matthew J. 
Published: September 2010

Abstract
Purpose: To compare clinical, immunohistochemical (IHC), and gene expression models of prognosis applicable to formalin-fixed, paraffin-embedded blocks in a large series of estrogen receptor (ER)–positive breast cancers from patients uniformly treated with adjuvant tamoxifen.
Experimental Design: Quantitative real-time reverse transcription-PCR (qRT-PCR) assays for 50 genes identifying intrinsic breast cancer subtypes were completed on 786 specimens linked to clinical (median follow-up, 11.7 years) and IHC [ER, progesterone receptor (PR), HER2, and Ki67] data. Performance of predefined intrinsic subtype and risk-of-relapse scores was assessed using multivariable Cox models and Kaplan-Meier analysis. Harrell's C-index was used to compare fixed models trained in independent data sets, including proliferation signatures.
Results: Despite clinical ER positivity, 10% of cases were assigned to nonluminal subtypes. qRT-PCR signatures for proliferation genes gave more prognostic information than clinical assays for hormone receptors or Ki67. In Cox models incorporating standard prognostic variables, hazard ratios for breast cancer disease-specific survival over the first 5 years of follow-up, relative to the most common luminal A subtype, are 1.99 [95% confidence interval (CI), 1.09-3.64] for luminal B, 3.65 (95% CI, 1.64-8.16) for HER2-enriched subtype, and 17.71 (95% CI, 1.71-183.33) for the basal-like subtype. For node-negative disease, PAM50 qRT-PCR–based risk assignment weighted for tumor size and proliferation identifies a group with &gt;95% 10-year survival without chemotherapy. In node-positive disease, PAM50-based prognostic models were also superior.
Conclusion: The PAM50 gene expression test for intrinsic biological subtype can be applied to large series of formalin-fixed, paraffin-embedded breast cancers, and gives more prognostic information than clinical factors and IHC using standard cut points. Clin Cancer Res; 16(21); 5222–32. ©2010 AACR.
Regulation of Cell Cycle Genes and Induction of Senescence by Overexpression of OTX2 in Medulloblastoma Cell Lines
Authors: Bunt Jens , de Haas Talitha G. , Hasselt Nancy E. , Zwijnenburg Danny A. , Koster Jan , Versteeg Rogier , Kool Marcel 
Published: September 2010

AbstractThe transcription factor orthodenticle homeobox 2 (OTX2) has been implicated in the pathogenesis of medulloblastoma, as it is often highly expressed and sometimes amplified in these tumors. Little is known of the downstream pathways regulated by OTX2. We therefore generated MED8A and DAOY medulloblastoma cell lines with doxycycline-inducible OTX2 expression. In both cell lines, OTX2 inhibited proliferation and induced a senescence-like phenotype with senescence-associated β-galactosidase activity. Expression profiles of time series after OTX2 induction in MED8A showed early upregulation of cell cycle genes related to the G2-M phase, such as AURKA, CDC25C, and CCNG2. Paradoxically, G1-S phase genes such as MYC, CDK4, CDK6, CCND1, and CCND2 were strongly downregulated, in line with the observed G1 arrest. ChIP-on-chip analyses of OTX2 binding to promoter regions in MED8A and DAOY showed a strong enrichment for binding to the G2-M genes, suggesting a direct activation. Their mRNA expression correlated with OTX2 expression in primary tumors, underscoring the in vivo relevance of this regulation. OTX2 induction activated the P53 pathway in MED8A, but not in DAOY, which carries a mutated P53 gene. In DAOY cells, senescence-associated secretory factors, such as interleukin-6 and insulin-like growth factor binding protein 7, were strongly upregulated after OTX2 induction. We hypothesize that the imbalance in cell cycle stimulation by OTX2 leads to cellular senescence either by activating the P53 pathway or through the induction of secretory factors. Our data indicate that OTX2 directly induces a series of cell cycle genes but requires cooperating genes for an oncogenic acceleration of the cell cycle. Mol Cancer Res; 8(10); 1344–57. ©2010 AACR.
Long-Term Benefit of Primary Prevention With an Implantable Cardioverter-Defibrillator
Authors: Goldenberg Ilan , Gillespie John , Moss Arthur J. , Hall W. Jackson , Klein Helmut , McNitt Scott , Brown Mary W. , Cygankiewicz Iwona , Zareba Wojciech ,   and the Executive Committee of the Multicenter Automatic Defibrillator Implantation Trial II
Published: September 2010

Background—
The Multicenter Automatic Defibrillator Implantation Trial II (MADIT-II) showed a significant 31 reduction in the risk of death with primary implantable cardioverter-defibrillator (ICD) therapy during a median follow-up of 1.5 years. However, currently there are no data on the long-term efficacy of primary defibrillator therapy.

Methods and Results—

MADIT-II enrolled 1232 patients with ischemic left ventricular dysfunction who were randomized to ICD and non-ICD medical therapy and were followed up through November 2001. For the present long-term study, we acquired posttrial mortality data through March 2009 for all study participants (median follow-up, 7.6 years). Multivariate Cox proportional hazards regression modeling was performed to calculate the hazard ratio for ICD versus non-ICD therapy during long-term follow-up. At 8 years of follow-up, the cumulative probability of all-cause mortality was 49 among patients treated with an ICD compared with 62 among non-ICD patients (
P
<0.001). Multivariate analysis demonstrated that ICD therapy was associated with a significant long-term survival benefit (hazard ratio for 0- through 8-year mortality=0.66 [95 confidence interval, 0.56 to 0.78];
P
<0.001). Treatment with an ICD was shown to be associated with a significant reduction in the risk of death during the early phase of the extended follow-up period (0 through 4 years: hazard ratio=0.61 [95 confidence interval, 0.50 to 0.76];
P
<0.001) and with continued life-saving benefit during the late phase of follow-up (5 through 8 years: hazard ratio=0.74 [95 confidence interval, 0.57 to 0.96];
P
=0.02).

Conclusions—
Our findings demonstrate a sustained 8-year survival benefit with primary ICD therapy in the MADIT-II population.
Observations, Simulations, and Dynamics of Jet Stream Variability and Annular Modes
Authors: Kidston Joseph , Frierson D. M. W. , Renwick J. A. , Vallis G. K. 
Published: September 2010

Abstract
The characteristics of the dominant pattern of extratropical variability (the so-called annular modes) are examined in the context of the theory that eddy-driven jets are self-maintaining. It is shown that there is genuine hemispheric symmetry in the variation of the zonal wind in the Southern Hemisphere but not the Northern Hemisphere. The annular mode is shown to be baroclinic in nature; it is associated with changes in the baroclinic eddy source latitude, and the latitude of the eddy source region is organized by the mean flow. This behavior is expected if there is a baroclinic feedback that encourages the maximum baroclinic instability to be coincident with the maximum zonal wind speed, and discourages the meridional vacillation of the eddy-driven jet stream. It is shown that the strength of the thermally indirect circulation that gives rise to the baroclinic feedback appears to influence the time scale of the annular mode. When the thermally indirect circulation is stronger the annular mode has a longer e-folding time in a simplified GCM. Preliminary results indicate that the same dynamics are important in the real atmosphere.
A New Method to Estimate the Systematical Biases of Expendable Bathythermograph
Authors: Cheng Lijing , Zhu Jiang , Reseghetti Franco , Liu Qingping 
Published: September 2010

Abstract
A new technique to estimate three major biases of XBT probes (improper fall rate, start-up transient, and pure temperature error) has been developed. Different from the well-known and standard “temperature error free” differential method, the new method analyses temperature profiles instead of vertical gradient temperature profiles. Consequently, it seems to be more noise resistant because it uses the integral property over the entire vertical profile instead of gradients. Its validity and robustness have been checked in two ways. In the first case, the new integral technique and the standard differential method have been applied to a set of simulated XBT profiles having a known fall-rate equation to which various combinations of pure temperature errors, random errors, and spikes have been added for the sake of this simulation. Results indicated that the single pure temperature error has little impact on the fall-rate coefficients for both methods, whereas with the added random error and spikes the simulation leads to better results with the new integral technique than with the standard differential method. In the second case, two sets of profiles from actual XBT versus CTD comparisons, collected near Barbados in 1990 and in the western Mediterranean (2003–04 and 2008–09), have been used. The individual fall-rate coefficients and start-up transient for each XBT profile, along with the overall pure temperature correction, have been calculated for the XBT profiles. To standardize procedures and to improve the terms of comparison, the individual start-up transient estimated by the integral method was also assigned and included in calculations with the differential method. The new integral method significantly reduces both the temperature difference between XBT and CTD profiles and the standard deviation. Finally, the validity of the mean fall-rate coefficients and the mean start-up transient, respectively, for DB and T7 probes as precalculated equations was verified. In this case, the temperature difference is reduced to less than 0.1°C for both datasets, and it randomly distributes around the null value. In addition, the standard deviation on depth values is largely reduced, and the maximum depth error computed with the datasets near Barbados is within 1.1% of its real value. Results also indicate that the integral method has a good performance mainly when applied to profiles in regions with either a very large temperature gradient, at the thermocline or a very small one, toward the bottom.
A Retrospective Evaluation of the Storm Surge Produced by Hurricane Gustav (2008): Forecast and Hindcast Results
Authors: Forbes Cristina , Luettich Richard A. , Mattocks Craig A. , Westerink Joannes J. 
Published: September 2010

Abstract
The evolution and convergence of modeled storm surge were examined using a high-resolution implementation of the Advanced Circulation Coastal Ocean and Storm Surge (ADCIRC) model for Hurricane Gustav (2008). The storm surge forecasts were forced using an asymmetric gradient wind model (AWM), directly coupled to ADCIRC at every time step and at every grid node. A total of 20 forecast advisories and best-track data from the National Hurricane Center (NHC) were used as input parameters into the wind model. Differences in maximum surge elevations were evaluated for ensembles comprised of the final 20, 15, 10, and 5 forecast advisories plus the best track. For this particular storm, the final 10–12 forecast advisories, encompassing the last 2.5–3 days of the storm’s lifetime, give a reasonable estimate of the final storm surge and inundation. The results provide a detailed perspective of the variability in the storm surge due to variability in the meteorological forecast and how this changes as the storm approaches landfall. This finding is closely tied to the consistency and accuracy of the NHC storm track forecasts and the predicted landfall location and, therefore, cannot be generalized to all storms in all locations. Nevertheless, this first attempt to translate variability in forecast meteorology into storm surge variability provides useful insights for guiding the potential use of storm surge models for forecast purposes. Model skill was also evaluated for Hurricane Gustav by comparing observed water levels with hindcast modeled water levels forced by river flow, tides, and several sources of wind data. The AWM (which ingested best-track information from NHC) generated winds that were slightly higher than those from NOAA’s Hurricane Research Division (HRD) H*Wind analyses and substantially greater than the North American Mesoscale (NAM) model. Surge obtained using the AWM more closely matched the observed water levels than that computed using H*Wind; however, this may be due to the neglect of the contribution of wave setup to the surge, especially in exposed areas. Several geographically distinct storm surge response regimes, some characterized by multisurge pulses, were identified and described.
Knowledge about pandemic influenza in healthcare and non-healthcare students in London
Authors: Purssell Edward , While Alison 
Published: September 2010

Objective: To investigate the knowledge of university students regarding pandemic and seasonal influenza. Design: Online questionnaire-based survey of undergraduate and postgraduate students, including those on nursing, medical, other health and non-health related courses. Method: The sample was recruited using the university email system, and the survey was administered using SurveyMonkey. The questionnaire sought the following data: demographics; general knowledge; intentions with regards to vaccines, pharmacological and behavioural interventions; personal susceptibility and the symptoms of influenza; and the provision of information. Results: Approximately half (56 per cent) of respondents were on health-related courses. There was a good level of knowledge about influenza and its severity, and the importance of vaccination, although few intended actually receiving the seasonal or pandemic vaccines (23 per cent and 21 per cent respectively). However, in the event of a pandemic most students would still attend college (60 per cent) and almost half would still attend social events (47 per cent). Many thought that there had been hype by the government (44 per cent) and the media (89 per cent). Conclusions: There was a good level of knowledge about influenza, although this was not always reflected in intended behaviours with regards to vaccination and isolation.
Media literacy and cigarette smoking in Hungarian adolescents
Authors: Page Randy M , Piko Bettina F , Balazs Mate A , Struk Tamara 
Published: September 2010

Objective: To assess smoking media literacy in a sample of Hungarian youth and to determine its association with current smoking and susceptibility to future smoking. Design: Quantitative cross-sectional survey. Setting: Four elementary and four high schools in Mako, Hungary. Method: A survey form was administered in regularly-scheduled classes to 546 eighth- and twelfth-grade students that included the smoking media literacy (SML) scale and items assessing cigarette use. Logistic regression was used to examine the relationship of smoking media literacy with current smoking, and also separately for susceptibility to smoking in the future, as dependent dichotomous variables. Results: Smoking media literacy was lower among the Hungarian adolescents than what has been previously reported in American adolescents. Multivariate logistic regression analysis results showed smoking media literacy to be associated with reduced risk of current smoking status at a similar level to that found in American adolescents. However, unlike previous research in American adolescents, smoking media literacy and susceptibility to future smoking was not associated. Reduced smoking may be most associated with the representation-reality domain of media literacy, which relates recognition of what is portrayed in the media with reality. Conclusion: Based on this study’s findings, prevention and health promotion planners in Hungary should consider media literacy training as a possible addition to smoking prevention efforts in community- and school-based efforts.
Phosphatidylinositol 3 kinase modulation of trophoblast cell differentiation
Authors: Kent Lindsey N , Konno Toshihiro , Soares Michael J 
Published: September 2010

AbstractBackgroundThe trophoblast lineage arises as the first differentiation event during embryogenesis. Trophoblast giant cells are one of several end-stage products of trophoblast cell differentiation in rodents. These cells are located at the maternal-fetal interface and are capable of invasive and endocrine functions, which are necessary for successful pregnancy. Rcho-1 trophoblast stem cells can be effectively used as a model for investigating trophoblast cell differentiation. In this report, we evaluated the role of the phosphatidylinositol 3-kinase (PI3K) signaling pathway in the regulation of trophoblast cell differentiation. Transcript profiles from trophoblast stem cells, differentiated trophoblast cells, and differentiated trophoblast cells following disruption of PI3K signaling were generated and characterized.ResultsProminent changes in gene expression accompanied the differentiation of trophoblast stem cells. PI3K modulated the expression of a subset of trophoblast cell differentiation-dependent genes. Among the PI3K-responsive genes were those encoding proteins contributing to the invasive and endocrine phenotypes of trophoblast giant cells.ConclusionsGenes have been identified with differential expression patterns associated with trophoblast stem cells and trophoblast cell differentiation; a subset of these genes are regulated by PI3K signaling, including those impacting the differentiated trophoblast giant cell phenotype.
Gene signatures in wound tissue as evidenced by molecular profiling in the chick embryo model
Authors: Soulet Fabienne , Kilarski Witold W , Antczak Philipp , Herbert John , Bicknell Roy , Falciani Francesco , Bikfalvi Andreas 
Published: September 2010

Abstract

Background
Modern functional genomic approaches may help to better understand the molecular events involved in tissue morphogenesis and to identify molecular signatures and pathways. We have recently applied transcriptomic profiling to evidence molecular signatures in the development of the normal chicken chorioallantoic membrane (CAM) and in tumor engrafted on the CAM. We have now extended our studies by performing a transcriptome analysis in the "wound model" of the chicken CAM, which is another relevant model of tissue morphogenesis.

Results
To induce granulation tissue (GT) formation, we performed wounding of the chicken CAM and compared gene expression to normal CAM at the same stage of development. Matched control samples from the same individual were used. We observed a total of 282 genes up-regulated and 44 genes down-regulated assuming a false-discovery rate at 5% and a fold change > 2. Furthermore, bioinformatics analysis lead to the identification of several categories that are associated to organismal injury, tissue morphology, cellular movement, inflammatory disease, development and immune system. Endothelial cell data filtering leads to the identification of several new genes with an endothelial cell signature.

Conclusions
The chick chorioallantoic wound model allows the identification of gene signatures and pathways involved in GT formation and neoangiogenesis. This may constitute a fertile ground for further studies.