bluuebunny/crossref_metadata_2025_split huggingface dataset:
Transformation-Dependent Silencing of Tumor-Selective Apoptosis-Inducing TRAIL by DNA Hypermethylation Is Antagonized by Decitabine
Authors: Lund Per , Kotova Irina , Kedinger Valérie , Khanwalkar Harshal , Voltz Emilie , Hahn William C. , Gronemeyer Hinrich 
Published: June 2011

Abstract
TNF-related apoptosis-inducing ligand (TRAIL) kills tumor cells selectively. We asked how emerging tumor cells escape elimination by TRAIL and how tumor-specific killing by TRAIL could then be restored. We found that TRAIL expression is consistently downregulated in HRASG12V-transformed cells in stepwise tumorigenesis models derived from four different tissues due to DNA hypermethylation of CpG clusters within the TRAIL promoter. Decitabine de-silenced TRAIL, which remained inducible by interferon, while induction of TRAIL by blocking the HRASG12V-activated mitogen-activated protein kinase pathway was subordinated to epigenetic silencing. Decitabine induced apoptosis through upregulation of endogenous TRAIL in cooperation with favorable regulation of key players acting in TRAIL-mediated apoptosis. Apoptosis induction by exogenously added TRAIL was largely increased by decitabine. In vivo treatment of xenografted human HRASG12V-transformed human epithelial kidney or syngenic mice tumors by decitabine blocked tumor growth induced TRAIL expression and apoptosis. Our results emphasize the potential of decitabine to enhance TRAIL-induced apoptosis in tumors and thus provide a rationale for combination therapies with decitabine to increase tumor-selective apoptosis. Mol Cancer Ther; 10(9); 1611–23. ©2011 AACR.
Impact of Enhanced Satellite-Derived Atmospheric Motion Vector Observations on Numerical Tropical Cyclone Track Forecasts in the Western North Pacific during TPARC/TCS-08
Authors: Berger Howard , Langland Rolf , Velden Christopher S. , Reynolds Carolyn A. , Pauley Patricia M. 
Published: June 2011

AbstractEnhanced atmospheric motion vectors (AMVs) produced from the geostationary Multifunctional Transport Satellite (MTSAT) are assimilated into the U.S. Navy Operational Global Atmospheric Prediction System (NOGAPS) to evaluate the impact of these observations on tropical cyclone track forecasts during the simultaneous western North Pacific Ocean Observing System Research and Predictability Experiment (THORPEX) Pacific Asian Regional Campaign (TPARC) and the Tropical Cyclone Structure—2008 (TCS-08) field experiments. Four-dimensional data assimilation is employed to take advantage of experimental high-resolution (space and time) AMVs produced for the field campaigns by the Cooperative Institute for Meteorological Satellite Studies. Two enhanced AMV datasets are considered: 1) extended periods produced at hourly intervals over a large western North Pacific domain using routinely available MTSAT imagery and 2) limited periods over a smaller storm-centered domain produced using special MTSAT rapid-scan imagery. Most of the locally impacted forecast cases involve Typhoons Sinlaku and Hagupit, although other storms are also examined. On average, the continuous assimilation of the hourly AMVs reduces the NOGAPS tropical cyclone track forecast errors—in particular, for forecasts longer than 72 h. It is shown that the AMVs can improve the environmental flow analyses that may be influencing the tropical cyclone tracks. Adding rapid-scan AMV observations further reduces the NOGAPS forecast errors. In addition to their benefit in traditional data assimilation, the enhanced AMVs show promise as a potential resource for advanced objective data-targeting methods.
The Role of Linear Interference in Northern Annular Mode Variability Associated with Eurasian Snow Cover Extent
Authors: Smith Karen L. , Kushner Paul J. , Cohen Judah 
Published: June 2011

AbstractOne of the outstanding questions regarding the observed relationship between October Eurasian snow cover anomalies and the boreal winter northern annular mode (NAM) is what causes the multiple-week lag between positive Eurasian snow cover anomalies in October and the associated peak in Rossby wave activity flux from the troposphere to the stratosphere in December. This study explores the following hypothesis about this lag: in order to achieve amplification of the wave activity, the vertically propagating Rossby wave train associated with the snow cover anomaly must reinforce the climatological stationary wave, which corresponds to constructive linear interference between the anomalous wave and the climatological wave. It is shown that the lag in peak wave activity flux arises because the Rossby wave train associated with the snow cover is in quadrature or out of phase with the climatological stationary wave from October to mid-November. Beginning in mid-November the associated wave anomaly migrates into a position that is in phase with the climatological wave, leading to constructive interference and anomalously positive upward wave activity fluxes until mid-January. Climate models from the Coupled Model Intercomparison Project 3 (CMIP3) do not capture this behavior. This linear interference effect is not only associated with stratospheric variability related to Eurasian snow cover anomalies but is a general feature of Northern Hemisphere troposphere–stratosphere interactions and, in particular, dominated the negative NAM events of the fall–winter of 2009/10.
The Dependence of Storm Longevity on the Pattern of Deep Convection Initiation in a Low-Shear Environment
Authors: Houston Adam L. , Wilhelmson Robert B. 
Published: June 2011

Abstract
The sensitivity of storm longevity to the pattern of deep convection initiation (e.g., multiple, quasi-linearly arranged initial deep convective cells versus an isolated deep convective cell) is examined using idealized cloud-resolving simulations conducted with a low-shear initial environment. When multiple deep convective cells are initialized in close proximity to one another using either a line of thermals or a shallow airmass boundary, long-lived storms are produced. However, when isolated deep convection is initiated, the resultant storm steadily decays following initiation. These results illustrate that a quasi-linear mechanism, such as a preexisting airmass boundary, that initiates multiple deep convective cells in close proximity can lead to longer-lived storms than a mechanism that initiates isolated deep convection.
The essential difference between the experiments conducted is that an isolated initial storm produces a shallower cold pool than when a quasi-linear initiation is used. It is argued that the deep cold pools promote deep forced ascent, systematic convective cell redevelopment, and thus long-lived storms, even in environments with small values of vertical shear. The difference in cold pool depth between the simulations is attributed to differences in the horizontal flux of cold air to the gust front. With a single initial storm, the few convective cells that subsequently form provide only a limited source of cold air, leading to a cold pool that is shallow and incapable of fostering continued updraft redevelopment.
Water Budget of Typhoon Nari (2001)
Authors: Yang Ming-Jen , Braun Scott A. , Chen Deng-Shun 
Published: June 2011

Abstract
Although there have been many observational and modeling studies of tropical cyclones (TCs), the understanding of TCs’ budgets of vapor and condensate and the changes of budgets after TCs’ landfall is still quite limited. In this study, high-resolution (2-km horizontal grid size and 2-min data interval) model output from a cloud-resolving simulation of Typhoon Nari (2001) is used to examine the vapor and condensate budgets and the respective changes of the budgets after Nari’s landfall on Taiwan. All budget terms are directly derived from the model except for a small residual term. For the vapor budget, while Nari is over the ocean, evaporation from the ocean surface is 11% of the inward horizontal vapor transport within 150 km of the storm center, and the net horizontal vapor convergence into the storm is 88% of the net condensation. The ocean source of water vapor in the inner core is a small portion (5.5%) of horizontal vapor import, consistent with previous studies. After landfall, Taiwan’s steep terrain enhances Nari’s secondary circulation significantly and produces stronger horizontal vapor import at low levels, resulting in a 22% increase in storm-total condensation. Precipitation efficiency, defined from either the large-scale or microphysics perspective, is increased 10%–20% over the outer-rainband region after landfall, in agreement with the enhanced surface rainfall over the complex terrain.
Predictors of non-remission of depression in a palliative care population
Authors: Goodwin Laura , Lee William , Price Annabel , Rayner Lauren , Monroe Barbara , Sykes Nigel , Hansford Penny , Higginson Irene J , Hotopf Matthew 
Published: June 2011

Background: Prospective studies of depression in palliative care are rare. Two studies that examine depression prospectively in patients with advanced disease have not looked at predictors of remission. Aims: to explore prospective predictors of non-remission of depression in palliative care. Design and participants: The study design comprised two data collections: initial assessment on referral to a palliative care service in South London, UK, and a four-week follow-up. Seventy six participants met the criteria for ‘any depressive syndrome’ at the time 1 assessment, using the PRIME-MD, who also participated at time 2. The outcome measure was remission ( N = 39) or non-remission ( N = 37) of depression by time 2. Results: The findings showed that reporting low social support from family and friends at time of referral was the most powerful risk factor for non-remission. There was also a strong association between improved physical symptoms, from time 1 to 2, and remission of depression. Conclusions: This study in palliative care is the first of which we are aware to explore factors associated with non-remission of depression. Depressed patients identified with low social support on referral to palliative care services might particularly benefit from additional psychosocial care in the treatment of their depression. This study provides evidence that effective physical symptom management in palliative care may be a valuable intervention for depressive symptoms.
Hydrodynamic analysis models for the design of Darrieus-type vertical-axis marine current turbines
Authors: Dai Y M , Gardiner N , Sutton R , Dyson P K 
Published: June 2011

This work reviews hydrodynamic analysis models developed for the design of Darrieus-type vertical axis marine current turbines, with particular emphasis on the prediction of hydrodynamic rotor performance, as well as their suitability for aiding the optimization process, either directly, or as a fast filter of potential blade profiles. In order to improve the performance of a marine current turbine it is necessary accurately to model the flow passing the turbine’s blades. Several types of models exist for Darrieus-type turbines, from momentum-based streamtube models to complex computational fluids dynamics (CFD) simulations. With continuously varying large angles of attack on the blades, the main issue is accurate prediction of the flow field around the rotor and thus its loads and torque. This is further complicated by the significant inherent unsteady hydrodynamic characteristics and potential for dynamic stall. Comparisons of the analytical results with experimental data are presented to compare these different models and thus illustrate their areas of suitability in this context. In conclusion, vertical axis machines have the potential of high power capture compared with that of their horizontal counterparts but this will depend on blade profile and design configuration, solidity, and tip speed ratio. None of the existing theoretical methods really captures the actual performance of the machines except for detailed CFD simulations, which are inevitably computational time intensive.
Exercise training improves neurovascular control and functional capacity in heart failure patients regardless of age
Authors: Antunes-Correa Ligia M , Kanamura Bianca Y , Melo Ruth C , Nobre Thais S , Ueno Linda M , Franco Fabio GM , Roveda Fabiana , Braga Ana Maria , Rondon Maria UPB , Brum Patricia C , Barretto Antonio CP , Middlekauff Holly R , Negrao Carlos E 
Published: June 2011

Background: Exercise training is a non-pharmacological strategy for treatment of heart failure. Exercise training improves functional capacity and quality of life in patients. Moreover, exercise training reduces muscle sympathetic nerve activity (MSNA) and peripheral vasoconstriction. However, most of these studies have been conducted in middle-aged patients. Thus, the effects of exercise training in older patients are much less understood. The present study was undertaken to investigate whether exercise training improves functional capacity, muscular sympathetic activation and muscular blood flow in older heart failure patients, as it does in middle-aged heart failure patients. Design: Fifty-two consecutive outpatients with heart failure from the database of the Unit of Cardiovascular Rehabilitation and Physiology Exercise were divided by age (middle-aged, defined as 45–59 years, and older, defined as 60–75 years) and exercise status (trained and untrained). Methods: MSNA was recorded directly from the peroneal nerve using the microneurography technique. Forearm Blood Flow (FBF) was measured by venous occlusion plethysmography. Functional capacity was evaluated by cardiopulmonary exercise test. Results: Exercise training significantly and similarly increased FBF and peak VO2 in middle-aged and older heart failure patients. In addition, exercise training significantly and similarly reduced MSNA and forearm vascular resistance in these patients. No significant changes were found in untrained patients. Conclusion: Exercise training improves neurovascular control and functional capacity in heart failure patients regardless of age.
Identification of a truncated form of methionine sulfoxide reductase a expressed in mouse embryonic stem cells
Authors: Jia Pingping , Zhang Chi , Jia Yuanyuan , Webster Keith A , Huang Xupei , Kochegarov Andrei A , Lemanski Sharon L , Lemanski Larry F 
Published: June 2011

Abstract

Background
Methionine Sulfoxide Reductase A (MsrA), an enzyme in the Msr gene family, is important in the cellular anti-oxidative stress defense mechanism. It acts by reducing the oxidized methionine sulfoxide in proteins back to sulfide and by reducing the cellular level of reactive oxygen species. MsrA, the only enzyme in the Msr gene family that can reduce the S-form epimers of methionine sulfoxide, has been located in different cellular compartments including mitochondria, cytosol and nuclei of various cell lines.

Methods
In the present study, we have isolated a truncated form of the MsrA transcript from cultured mouse embryonic stem cells and performed eGFP fusion protein expression, confocal microscopy and real time RT-PCR studies.

Results
Results show a different expression response of this truncated transcript to oxygen deprivation and reoxygenation treatments in stem cells, compared to the longer full length form. In addition, a different subcellular localization pattern was noted with most of the eGFP fusion protein detected in the cytosol.

Conclusion
One possibility for the existence of a truncated form of the MsrA transcripts could be that with a smaller protein size, yet retaining a GCWFG action site, this protein might have easier access to oxidize methionine residues on proteins than the longer form of the MsrA protein, thus having an evolutionary selection advantage. This research opens the door for further study on the role and function of the truncated MsrA embryonic mouse stem cells.
Diagnostic utility of C-reactive Protein combined with brain natriuretic peptide in acute pulmonary edema: a cross sectional study
Authors: Komiya Kosaku , Ishii Hiroshi , Teramoto Shinji , Takahashi Osamu , Eshima Nobuoki , Yamaguchi Ou , Ebi Noriyuki , Murakami Junji , Yamamoto Hidehiko , Kadota Jun-ichi 
Published: June 2011

Abstract
Introduction Discriminating acute lung injury (ALI) or acute respiratory distress syndrome (ARDS) from cardiogenic pulmonary edema (CPE) using the plasma level of brain natriuretic peptide (BNP) alone remains controversial. The aim of this study was to determine the diagnostic utility of combination measurements of BNP and C-reactive protein (CRP) in critically ill patients with pulmonary edema.

Methods

This was a cross-sectional study. BNP and CRP data from 147 patients who presented to the emergency department due to acute respiratory failure with bilateral pulmonary infiltrates were analyzed.

Results

There were 53 patients with ALI/ARDS, 71 with CPE, and 23 with mixed edema. Median BNP and CRP levels were 202 (interquartile range 95-439) pg/mL and 119 (62-165) mg/L in ALI/ARDS, and 691 (416-1,194) pg/mL (p < 0.001) and 8 (2-42) mg/L (p < 0.001) in CPE. BNP or CRP alone offered good discriminatory performance (C-statistics 0.831 and 0.887), but the combination offered greater one [C-statistics 0.931 (p < 0.001 versus BNP) (p = 0.030 versus CRP)]. In multiple logistic-regression, BNP and CRP were independent predictors for the diagnosis after adjusting for other variables.

Conclusions

Measurement of CRP is useful as well as that of BNP for distinguishing ALI/ARDS from CPE. Furthermore, a combination of BNP and CRP can provide higher accuracy for the diagnosis.
The enigmatic mitochondrial genome of Rhabdopleura compacta(Pterobranchia) reveals insights into selection of an efficient tRNA system and supports monophyly of Ambulacraria
Authors: Perseke Marleen , Hetmank Joerg , Bernt Matthias , Stadler Peter F , Schlegel Martin , Bernhard Detlef 
Published: June 2011

Abstract

Background
The Hemichordata comprises solitary-living Enteropneusta and colonial-living Pterobranchia, sharing morphological features with both Chordata and Echinodermata. Despite their key role for understanding deuterostome evolution, hemichordate phylogeny is controversial and only few molecular data are available for phylogenetic analysis. Furthermore, mitochondrial sequences are completely lacking for pterobranchs. Therefore, we determined and analyzed the complete mitochondrial genome of the pterobranch Rhabdopleura compacta to elucidate deuterostome evolution. Thereby, we also gained important insights in mitochondrial tRNA evolution.

Results
The mitochondrial DNA of Rhabdopleura compacta corresponds in size and gene content to typical mitochondrial genomes of metazoans, but shows the strongest known strand-specific mutational bias in the nucleotide composition among deuterostomes with a very GT-rich main-coding strand. The order of the protein-coding genes in R. compacta is similar to that of the deuterostome ground pattern. However, the protein-coding genes have been highly affected by a strand-specific mutational pressure showing unusual codon frequency and amino acid composition. This composition caused extremely long branches in phylogenetic analyses. The unusual codon frequency points to a selection pressure on the tRNA translation system to codon-anticodon sequences of highest versatility instead of showing adaptations in anticodon sequences to the most frequent codons. Furthermore, an assignment of the codon AGG to Lysine has been detected in the mitochondrial genome of R. compacta, which is otherwise observed only in the mitogenomes of some arthropods. The genomes of these arthropods do not have such a strong strand-specific bias as found in R. compacta but possess an identical mutation in the anticodon sequence of the tRNALys.

Conclusion
A strong reversed asymmetrical mutational constraint in the mitochondrial genome of Rhabdopleura compacta may have arisen by an inversion of the replication direction and adaptation to this bias in the protein sequences leading to an enigmatic mitochondrial genome. Although, phylogenetic analyses of protein coding sequences are hampered, features of the tRNA system of R. compacta support the monophyly of Ambulacraria. The identical reassignment of AGG to Lysine in two distinct groups may have occurred by convergent evolution in the anticodon sequence of the tRNALys.
Multiple platform assessment of the EGF dependent transcriptome by microarray and deep tag sequencing analysis
Authors: Llorens Franc , Hummel Manuela , Pastor Xavier , Ferrer Anna , Pluvinet Raquel , Vivancos Ana , Castillo Ester , Iraola Susana , Mosquera Ana M , González Eva , Lozano Juanjo , Ingham Matthew , Dohm Juliane C , Noguera Marc , Kofler Robert , del Río Jose Antonio , Bayés Mònica , Himmelbauer Heinz , Sumoy Lauro 
Published: June 2011

AbstractBackgroundEpidermal Growth Factor (EGF) is a key regulatory growth factor activating many processes relevant to normal development and disease, affecting cell proliferation and survival. Here we use a combined approach to study the EGF dependent transcriptome of HeLa cells by using multiple long oligonucleotide based microarray platforms (from Agilent, Operon, and Illumina) in combination with digital gene expression profiling (DGE) with the Illumina Genome Analyzer.ResultsBy applying a procedure for cross-platform data meta-analysis based on RankProd and GlobalAncova tests, we establish a well validated gene set with transcript levels altered after EGF treatment. We use this robust gene list to build higher order networks of gene interaction by interconnecting associated networks, supporting and extending the important role of the EGF signaling pathway in cancer. In addition, we find an entirely new set of genes previously unrelated to the currently accepted EGF associated cellular functions.ConclusionsWe propose that the use of global genomic cross-validation derived from high content technologies (microarrays or deep sequencing) can be used to generate more reliable datasets. This approach should help to improve the confidence of downstreamin silicofunctional inference analyses based on high content data.