bluuebunny/crossref_metadata_2025_split huggingface dataset:
Preclinical Evaluation of Biopolymer-Delivered Circulating Angiogenic Cells in a Swine Model of Hibernating Myocardium
Authors: Giordano Céline , Thorn Stephanie L. , Renaud Jennifer M. , Al-Atassi Talal , Boodhwani Munir , Klein Ran , Kuraitis Drew , Dwivedi Girish , Zhang Pingchuan , DaSilva Jean N. , Ascah Kathryn J. , deKemp Robert A. , Suuronen Erik J. , Beanlands Rob S.B. , Ruel Marc 
Published: October 2013

Background—
Vasculogenic cell–based therapy combined with tissue engineering is a promising revascularization approach targeted at patients with advanced coronary artery disease, many of whom exhibit myocardial hibernation. However, to date, no experimental data have been available in this context; we therefore examined the biopolymer-supported delivery of circulating angiogenic cells using a clinically relevant swine model of hibernating myocardium.

Methods and Results—

Twenty-five swine underwent placement of an ameroid constrictor on the left circumflex artery. After 2 weeks, animals underwent echocardiography, rest and stress ammonia-positron emission tomography perfusion, and fluorodeoxyglucose positron emission tomography viability scans. The following week, swine were randomized to receive intramyocardial injections of PBS control (n=10), circulating angiogenic cells (n=8), or circulating angiogenic cells+collagen-based matrix (n=7). The imaging protocol was repeated after 7 weeks. Baseline positron emission tomography myocardial blood flow and myocardial flow reserve were reduced in the left circumflex artery territory (both
P
<0.001), and hibernation (mismatch) was observed. At follow-up, stress myocardial blood flow had increased (
P
≤0.01) and hibernation decreased (
P
<0.01) in the cells+matrix group only. Microsphere-measured myocardial blood flow validated the perfusion results. Arteriole density and wall motion abnormalities improved in the cells+matrix group. There was also a strong trend toward an improvement in ejection fraction (
P
=0.07).

Conclusions—
In this preclinical swine model of ischemic and hibernating myocardium, the combined delivery of circulating angiogenic cells and a collagen-based matrix restored perfusion, reduced hibernation, and improved myocardial wall motion.
Cardiopulmonary Resuscitation With Chest Compressions During Sustained Inflations
Authors: Schmölzer Georg M. , O’Reilly Megan , LaBossiere Joseph , Lee Tze-Fun , Cowan Shaun , Qin Sharon , Bigam David L. , Cheung Po-Yin 
Published: October 2013

Background—
Guidelines on neonatal resuscitation recommend 90 chest compressions (CCs) and 30 manual inflations (3:1) per minute in newborns. The study aimed to determine whether CC s during sustained inflations (SIs) improves the recovery of asphyxiated newborn piglets in comparison with coordinated 3:1 resuscitation.

Methods and Results—

Term newborn piglets (n=8/group) were anesthetized, intubated, instrumented, and exposed to 45-minute normocapnic hypoxia followed by asphyxia. Piglets were randomly assigned to receive either 3:1 resuscitation (3:1 group) or CCs during SIs (SI group) when the heart rate decreased to 25% of baseline. Piglets randomly assigned to the SI group received SIs with a pressure of 30 cm H
2
O for 30 s. During the SI, CCs at a rate of 120/min were provided. SI was interrupted after 30 s for 1 s before a further 30-s SI was provided. CCs were continued throughout SIs. CCs and SI were continued until the return of spontaneous circulation. Continuous respiratory parameters, cardiac output, mean systemic and pulmonary artery pressures, and regional blood flows were measured. Mean (standard deviation) time for return of spontaneous circulation was significantly reduced in SI group versus 3:1 group (32 [11] s versus 205 [113] s, respectively). In the SI group, administration of oxygen and epinephrine was significantly lower, whereas minute ventilation and exhaled CO
2
were significantly increased. The SI group had significantly higher mean systemic and pulmonary arterial pressures during resuscitation in comparison with the 3:1 group (51 [10] versus 31 [5] mm Hg; 41[7] versus 31 [7] mm Hg, respectively; all
P
<0.05), with improved cardiac output and carotid blood flow.

Conclusions—
Combining CCs and SIs significantly improved the return of spontaneous circulation with better hemodynamic recovery in asphyxiated newborn piglets in comparison with standard coordinated 3:1 resuscitation.
Origins of Tropical Pacific Decadal Variability: Role of Stochastic Atmospheric Forcing from the South Pacific*
Authors: Okumura Yuko M. 
Published: October 2013

Abstract
Based on the analysis of multicentury–millennium integrations of an atmospheric model coupled to the ocean with varying degrees, it is argued that ENSO-like decadal variability is primarily driven by stochastic atmospheric forcing. In particular, the leading mode of internal atmospheric variability over the South Pacific, which projects onto the Pacific–South American (PSA) pattern, plays an important role in modulating the trade winds and sea surface temperature (SST) in the southeast tropical Pacific. Subsequent ocean–atmosphere interactions organize a basinwide SST anomaly pattern in the tropics, which in turn forces atmospheric Rossby waves into the extratropics, reinforcing the PSA pattern and inducing coherent decadal changes in the North Pacific. In the absence of ocean dynamics, equatorial SST variability is reduced and the North Pacific exhibits decadal variability independent of the tropical–South Pacific. The strong tropical–South Pacific linkage may be attributed to the equatorially asymmetric nature of tropical Pacific climate.
Real-Time Measurement of the Range Correlation for Range Oversampling Processing
Authors: Curtis Christopher D. , Torres Sebastián M. 
Published: October 2013

AbstractAs range-oversampling processing has become more practical for weather radars, implementation issues have become important to ensure the best possible performance. For example, all of the linear transformations that have been utilized for range-oversampling processing directly depend on the normalized range correlation matrix. Hence, accurately measuring the correlation in range time is essential to avoid reflectivity biases and to ensure the expected variance reduction. Although the range correlation should be relatively stable over time, hardware changes and drift due to changing environmental conditions can have measurable effects on the modified pulse. To reliably track changes in the range correlation, an automated real-time method is needed that does not interfere with normal data collection. A method is proposed that uses range-oversampled data from operational radar scans and that works with radar returns from both weather and ground clutter. In this paper, the method is described, tested using simulations, and validated with time series data.
North Atlantic SST Anomalies and the Cold North European Weather Events of Winter 2009/10 and December 2010
Authors: Buchan Jian , Hirschi Joël J.-M. , Blaker Adam T. , Sinha Bablu 
Published: October 2013

AbstractNorthern Europe experienced consecutive periods of extreme cold weather in the winter of 2009/10 and in late 2010. These periods were characterized by a tripole pattern in North Atlantic sea surface temperature (SST) anomalies and exceptionally negative phases of the North Atlantic Oscillation (NAO). A global ocean–atmosphere general circulation model (OAGCM) is used to investigate the ocean’s role in influencing North Atlantic and European climate. Observed SST anomalies are used to force the atmospheric model and the resultant changes in atmospheric conditions over northern Europe are examined. Different atmospheric responses occur in the winter of 2009/10 and the early winter of 2010. These experiments suggest that North Atlantic SST anomalies did not significantly affect the development of the negative NAO phase in the cold winter of 2009/10. However, in November and December 2010 the large-scale North Atlantic SST anomaly pattern leads to a significant shift in the atmospheric circulation over the North Atlantic toward a NAO negative phase. Therefore, these results indicate that SST anomalies in November/December 2010 were particularly conducive to the development of a negative NAO phase, which culminated in the extreme cold weather conditions experienced over northern Europe in December 2010.
Stratospheric Analysis and Forecast Errors Using Hybrid and Sigma Coordinates
Authors: Eckermann Stephen D. , McCormack John P. , Ma Jun , Hogan Timothy F. , Zawdie Katherine A. 
Published: October 2013

Abstract
Past investigations have documented large divergent wind anomalies in stratospheric reanalyses over steep terrain, which were attributed to discretization errors produced by the terrain-following (sigma) vertical coordinate in the forecast model. However, forecasting experiments have reported negligible differences in skill between sigma- and hybrid-coordinate models. This leads to the paradoxical conclusion that discretization errors in the forecast model yield significant stratospheric analysis errors, but insignificant stratospheric forecast errors. The authors reexamine this issue by performing two forecast-assimilation experiments that are identical except for the vertical coordinate: one uses a sigma coordinate and the other uses a hybrid coordinate. The sigma-coordinate analyses exhibit large divergent wind anomalies over terrain that extend from the surface to the model top and distort explicitly resolved orographic gravity waves. Above the tropopause, divergent wind errors are suppressed by an order of magnitude or more in the hybrid-coordinate analyses. Over a 3-month period, stratospheric skill scores in the hybrid experiment show statistically significant improvements relative to the sigma experiment. Previous studies, which found no such differences, all used forecasts initialized from a common archived analysis. The results show that the dominant pathway for error growth and net skill impacts is via 0–9-h forecast backgrounds cycling successively through the data assimilation phase without significant observational correction. The skill impacts noted here should further motivate weather and climate models to adopt a hybrid coordinate with the best error suppression characteristics for a given modeling application.
ScreenSifter: analysis and visualization of RNAi screening data
Authors: Kumar Pankaj , Goh Germaine , Wongphayak Sarawut , Moreau Dimitri , Bard Frédéric 
Published: October 2013

Abstract

Background
RNAi screening is a powerful method to study the genetics of intracellular processes in metazoans. Technically, the approach has been largely inspired by techniques and tools developed for compound screening, including those for data analysis. However, by contrast with compounds, RNAi inducing agents can be linked to a large body of gene-centric, publically available data. However, the currently available software applications to analyze RNAi screen data usually lack the ability to visualize associated gene information in an interactive fashion.

Results
Here, we present ScreenSifter, an open-source desktop application developed to facilitate storing, statistical analysis and rapid and intuitive biological data mining of RNAi screening datasets. The interface facilitates meta-data acquisition and long-term safe-storage, while the graphical user interface helps the definition of a hit list and the visualization of biological modules among the hits, through Gene Ontology and protein-protein interaction analyses. The application also allows the visualization of screen-to-screen comparisons.

Conclusions
Our software package, ScreenSifter, can accelerate and facilitate screen data analysis and enable discovery by providing unique biological data visualization capabilities.
The 30-kDa and 38-kDa antigens from Mycobacterium tuberculosis induce partial maturation of human dendritic cells shifting CD4+ T cell responses towards IL-4 production
Authors: Heuer Marion , Behlich Anna-Sophie , Lee Ji-Sook , Ribechini Eliana , Jo Eun-Kyeong , Lutz Manfred B 
Published: October 2013

Abstract

Background

Mycobacterium tuberculosis (Mtb) infections are still a major cause of death among all infectious diseases. Although 99% of individuals infected with Mtb develop a CD4+ Th1 and CD8+ T cell mediated immunity as measured by tuberculin skin test, this results only in partial protection and Mtb vaccines are not effective. Deviation of immune responses by pathogens towards a Th2 profile is a common mechanism of immune evasion, typically leading to the persistence of the microbes.

Results
Here we tested the stimulatory capacity of selective Mtb antigens on human monocyte-derived dendritic cell (DC) maturation and cytokine production. DC maturation markers CD80, CD86 and CD83 were readily upregulated by H37Ra- and H37Rv-associated antigens, the 30-kDa (from Ag85 B complex) and 38-KDa Mtb antigens only partially induced these markers. All Mtb antigens induced variable levels of IL-6 and low levels of IL-10, there was no release of IL-12p70 detectable. Substantial IL-12p40 production was restricted to LPS or H37Ra and H37Rv preparations. Although the proliferation levels of primary T cell responses were comparable using all the differentially stimulated DC, the 30-kDa and 38-kDa antigens showed a bias towards IL-4 secretion of polarized CD4+ T cells after secondary stimulation as compared to H37Ra and H37Rv preparations.

Conclusion
Together our data indicate that 30-kDa and 38-kDa Mtb antigens induced only partial DC maturation shifting immune responses towards a Th2 profile.
The large soybean (Glycine max) WRKY TF family expanded by segmental duplication events and subsequent divergent selection among subgroups
Authors: Yin Guangjun , Xu Hongliang , Xiao Shuyang , Qin Yajuan , Li Yaxuan , Yan Yueming , Hu Yingkao 
Published: October 2013

Abstract

Background
WRKY genes encode one of the most abundant groups of transcription factors in higher plants, and its members regulate important biological process such as growth, development, and responses to biotic and abiotic stresses. Although the soybean genome sequence has been published, functional studies on soybean genes still lag behind those of other species.

Results
We identified a total of 133 WRKY members in the soybean genome. According to structural features of their encoded proteins and to the phylogenetic tree, the soybean WRKY family could be classified into three groups (groups I, II, and III). A majority of WRKY genes (76.7%; 102 of 133) were segmentally duplicated and 13.5% (18 of 133) of the genes were tandemly duplicated. This pattern was not apparent in Arabidopsis or rice. The transcriptome atlas revealed notable differential expression in either transcript abundance or in expression patterns under normal growth conditions, which indicated wide functional divergence in this family. Furthermore, some critical amino acids were detected using DIVERGE v2.0 in specific comparisons, suggesting that these sites have contributed to functional divergence among groups or subgroups. In addition, site model and branch-site model analyses of positive Darwinian selection (PDS) showed that different selection regimes could have affected the evolution of these groups. Sites with high probabilities of having been under PDS were found in groups I, II c, II e, and III. Together, these results contribute to a detailed understanding of the molecular evolution of the WRKY gene family in soybean.

Conclusions
In this work, all the WRKY genes, which were generated mainly through segmental duplication, were identified in the soybean genome. Moreover, differential expression and functional divergence of the duplicated WRKY genes were two major features of this family throughout their evolutionary history. Positive selection analysis revealed that the different groups have different evolutionary rates. Together, these results contribute to a detailed understanding of the molecular evolution of the WRKY gene family in soybean.
Long-term outcomes after nucleos(t)ide analogues discontinuation in chronic hepatitis B patients with HBeAg-negative
Authors: He Dengming , Guo Shimin , Chen Wen , Chen Xianli , Yan Guohua , Wang Jie , Li Maoshi , Zhu Peng , Huang Hongfei , Wang Yuming 
Published: October 2013

Abstract

Background
Hepatitis B e Antigen (HBeAg)-negative chronic hepatitis B (CHB) patients have an active liver disease with a high risk of progression to decompensated cirrhosis and hepatocellular carcinoma. The management strategy for HBeAg-negative CHB patients treated with nucleos(t)ide analogues (NUCs) is a topic of concern. To observe the outcomes for this population after NUCs withdrawal, HBeAg-negative CHB patients with loss of hepatitis B surface antigen (HBsAg) or sustained undetectable HBV DNA levels who had discontinued NUCs therapy were included in the study.

Methods
A total of 66 patients (2 patients with HBsAg loss and 64 patients with sustained undetectable HBV DNA levels) were examined. HBV DNA levels and alanine aminotransferase (ALT) levels were monitored regularly after discontinuation of NUCs therapy. Relapse was defined as HBV DNA levels >2,000 IU/mL while off therapy in at least two determinations more than 4 weeks apart.

Results
The time to achieve undetectable HBV DNA levels was 14 weeks (interquartile range (IQR): 12–24 weeks). The time until consolidation therapy was 144 weeks (IQR: 96–168 weeks). No relapses occurred in either of the HBsAg loss patients. Among the 64 patients with undetectable HBV DNA levels, 19 (29.7%) patients demonstrated evidence of relapse. All the relapses occurred within 96 weeks after discontinuation. The median duration of relapse was 36 weeks (IQR: 12–48 weeks). Elevation of HBV DNA and ALT levels over baseline was only observed in 10% of the relapse patients. There were no significant differences among the baseline characteristics (sex, HBV genotype, age, or ALT level) or the time until consolidation therapy between relapse and sustained-response patients.

Conclusions
NUC discontinuation is feasible after achieving undetectable HBV DNA levels in HBeAg-negative CHB patients. Prolonging the time until consolidation therapy may be a good strategy to decrease the rate of relapse. More than 96 weeks of sustained response is a predictive marker of long-term sustained response.
Potentially modifiable factors associated with non-adherence to phosphate binder use in patients on hemodialysis
Authors: Martins Maria Tereza Silveira , Silva Luciana Ferreira , Kraychete Angiolina , Reis Dandara , Dias Lidiane , Schnitman Gabriel , Oliveira Lívia , Lopes Gildete Barreto , Lopes Antonio Alberto 
Published: October 2013

Abstract

Background
Despite the evidence that phosphate binder (PB) is associated with improved outcomes many hemodialysis patients do not adhere to prescribed PB regimen. Therefore, barriers to PB adherence should be identified and eliminated. The purpose of this study was to evaluate PB adherence among hemodialysis patients and to explore potentially modifiable factors associated with low PB adherence.

Methods
A cross-sectional study (502 patients) was performed in four dialysis units in Salvador, Brazil, using data from the second phase of the Prospective Study of the Prognosis of Chronic Hemodialysis Patients (PROHEMO). Patients were categorized as adherent or non-adherent to PB based on their responses to a semi-structured questionnaire.

Results
Non-adherence to PB was observed for 65.7% of the patients. After adjustments for numerous covariates, cerebrovascular disease (odds ratio (OR), 3.30; 95% confidence interval (CI), 1.03-10.61), higher PTH (OR per each 300 pg/mL, 1.14; 95% CI, 1.01-1.28), lack of comprehension of the appropriate time to use PB (OR, 7.09; 95% CI, 2.10-23.95) and stopping PB use after feeling better (OR, 4.54; 95% CI, 1.45-14.25) or feeling worse (OR, 11.04; 95% CI, 1.79- 68.03) were significantly associated with PB non-adherence. By contrast, the adjusted odds of PB non-adherence were lower for patients with more years on dialysis (OR by each 2 years, 0.87; 95% CI, 0.80-0.95), with serum phosphorus above 5.5 mg/dL (OR, 0.53; 95% CI 0.34-0.82), who referred that were encouraged by the dialysis staff to be independent (OR, 0.52; 95% CI 0.30-0.90), and reported that the nephrologist explained how PB should be used (OR, 0.20; 95% CI 0.05-0.73).

Conclusion
The results of the present study are encouraging by showing evidence that improvement in the care provided by the dialysis staff and the attending nephrologist may play an important role in reducing the high prevalence of non-adherence to PB in maintenance hemodialysis patients. A new questionnaire is presented and may help to evaluate systematically the patients regarding PB adherence in hemodialysis setting.
Identification of genetic contribution to ischemic stroke by screening of single nucleotide polymorphisms in stroke patients by using a case control study design
Authors: Kumar Amit , Sagar Ram , Kumar Pradeep , Sahu Jitendra K , Grover Ashoo , Srivastava Achal K , Vivekanandhan S , Prasad Kameshwar 
Published: October 2013

Abstract

Background
Stroke is the second most common cause of death and disability worldwide. It is a multi-factorial disease influenced by both environmental and genetic factors. Studies from the different ethnic regions of world have reported variable results on association of Apolioprotein E (APOE), Methylenetetrahydrofolate reductase (MTHFR), Endothelial Nitric Oxide Synthase (ENOS), Factor V Leiden (F5), Cytochrome P450 4F2 (CYP4F2), beta-fibrinogen and Phosphodiesterase 4D (PDE4D) gene in stroke. There has been substantial evidence from the European descent genetic studies showing that genetic risk of stroke varies as per specific subtypes of ischemic stroke.
This study aims to test the hypothesis that above mentioned encoding gene polymorphisms are associated with stroke and to determine whether risk varies as per specific subtypes of stroke.

Methods/Design
The study design would be case–control study. Six hundred cases with diagnosis of stroke and 600 age and sex matched controls will be recruited. Controls will be matched in 1:1 ratio. Baseline and demographic data will be collected in standardized data collection form. Four ml of blood will be collected in EDTA coated vial and will be used for DNA isolation. Genotyping will be done by using PCR-RFLP method. For the reconfirmation of RFLP results, PCR product of each genotype in triplet for all the selected polymorphism will be sent for DNA sequencing. Data will be analyzed using conditional logistic regression to determine odds ratio associated with the above genes.

Discussion
This protocol will assess the association of above mentioned gene polymorphisms with ischemic stroke in North Indian Population. This study will also helpful to determine genetic component of stroke and whether variation in genetic risk as per different subtypes of stroke.