bluuebunny/crossref_metadata_2025_split huggingface dataset:
Changes in ENSO and Associated Overturning Circulations from Enhanced Greenhouse Gases by the End of the Twentieth Century
Authors: Ye Zhengqing , Hsieh William W. 
Published: April 2008

Abstract
With data from 12 coupled models in the Fourth Assessment Report (AR4) of the Intergovernmental Panel on Climate Change (IPCC), climate under year 2000 greenhouse gas (GHG) + aerosol forcing was compared with climate under preindustrial conditions. In the tropical Pacific, the warming in the mean sea surface temperatures (SST) was found to have an El Niño–like pattern, while both the equatorial zonal overturning circulation and the meridional overturning circulation weakened under increased GHG forcing.
For the El Niño–Southern Oscillation (ENSO), the asymmetry in the SST anomalies between El Niño and La Niña was found to be enhanced under increased GHG, for both the ensemble model data and the observed data (1900–99). Enhanced asymmetry between El Niño and La Niña was also manifested in the anomalies of the zonal wind stress, the equatorial undercurrent, and the meridional overturning circulation in the increased GHG simulations. The enhanced asymmetry in the model SST anomalies was mainly caused by the greatly intensified vertical nonlinear dynamic heating (NDH) anomaly (i.e., product of the vertical velocity anomaly and the negative vertical temperature gradient anomaly) during El Niño (but not during La Niña). Under increased GHG, the enhanced positive NDH anomalies during El Niño, when time averaged over the whole record, would change the SST mean state by an El Niño–like pattern.
Impact of the Incremental Analysis Updates on a Real-Time System of the North Atlantic Ocean
Authors: Benkiran M. , Greiner E. 
Published: April 2008

Abstract
Incremental analysis updates (IAUs) are a procedure by which analysis increments can be incorporated into a model hindcast and forecast in a smooth manner. It is similar to nudging but has a better response, particularly in regions of missing data. The IAU procedure was popular in the late 1990s in weather forecasting centers, because it acts as a low-pass filter. The impact of the IAU is examined in the context of a real-time, eddy-permitting ocean forecasting system in the North Atlantic from Mercator Océan. Forecast scores and ocean physics are compared for the following three companion runs: a forced mode, a sequential analysis, and IAU. These comparisons confirm that the IAU is beneficial because it removes spinup effects such as spurious waves and tropical convective cells. Forecast scores are also slightly improved. In addition, contrary to the weather forecasting case where the model and data are fairly unbiased, the IAU has the advantage of correcting the systematic biases in the ocean data assimilation system.
Estimation of the Minimum Canopy Resistance for Croplands and Grasslands Using Data from the 2002 International H2O Project
Authors: Alfieri Joseph G. , Niyogi Dev , Blanken Peter D. , Chen Fei , LeMone Margaret A. , Mitchell Kenneth E. , Ek Michael B. , Kumar Anil 
Published: April 2008

Abstract
Vegetated surfaces, such as grasslands and croplands, constitute a significant portion of the earth’s surface and play an important role in land–atmosphere exchange processes. This study focuses on one important parameter used in describing the exchange of moisture from vegetated surfaces: the minimum canopy resistance (rcmin). This parameter is used in the Jarvis canopy resistance scheme that is incorporated into the Noah and many other land surface models. By using an inverted form of the Jarvis scheme, rcmin is determined from observational data collected during the 2002 International H2O Project (IHOP_2002). The results indicate that rcmin is highly variable both site to site and over diurnal and longer time scales. The mean value at the grassland sites in this study is 96 s m−1 while the mean value for the cropland (winter wheat) sites is one-fourth that value at 24 s m−1. The mean rcmin for all the sites is 72 s m−1 with a standard deviation of 39 s m−1. This variability is due to both the empirical nature of the Jarvis scheme and a combination of changing environmental conditions, such as plant physiology and plant species composition, that are not explicitly considered by the scheme. This variability in rcmin has important implications for land surface modeling where rcmin is often parameterized as a constant. For example, the Noah land surface model parameterizes rcmin for the grasslands and croplands types in this study as 40 s m−1. Tests with the coupled Weather Research and Forecasting (WRF)–Noah model indicate that the using the modified values of rcmin from this study improves the estimates of latent heat flux; the difference between the observed and modeled moisture flux decreased by 50% or more. While land surface models that estimate transpiration using Jarvis-type relationships may be improved by revising the rcmin values for grasslands and croplands, updating the rcmin will not fully account for the variability in rcmin observed in this study. As such, it may be necessary to replace the Jarvis scheme currently used in many land surface and numerical weather prediction models with a physiologically based estimate of the canopy resistance.
Dominant negative Bmp5mutation reveals key role of BMPs in skeletal response to mechanical stimulation
Authors: Ho Andrew M , Marker Paul C , Peng Hairong , Quintero Andres J , Kingsley David M , Huard Johnny 
Published: April 2008

Abstract

Background
Over a hundred years ago, Wolff originally observed that bone growth and remodeling are exquisitely sensitive to mechanical forces acting on the skeleton. Clinical studies have noted that the size and the strength of bone increase with weight bearing and muscular activity and decrease with bed rest and disuse. Although the processes of mechanotransduction and functional response of bone to mechanical strain have been extensively studied, the molecular signaling mechanisms that mediate the response of bone cells to mechanical stimulation remain unclear.

Results
Here, we identify a novel germline mutation at the mouse Bone morphogenetic protein 5 (Bmp5) locus. Genetic analysis shows that the mutation occurs at a site encoding the proteolytic processing sequence of the BMP5 protein and blocks proper processing of BMP5. Anatomic studies reveal that this mutation affects the formation of multiple skeletal features including several muscle-induced skeletal sites in vivo. Biomechanical studies of osteoblasts from these anatomic sites show that the mutation inhibits the proper response of bone cells to mechanical stimulation.

Conclusion
The results from these genetic, biochemical, and biomechanical studies suggest that BMPs are required not only for skeletal patterning during embryonic development, but also for bone response and remodeling to mechanical stimulation at specific anatomic sites in the skeleton.
Rex1/Zfp42 is dispensable for pluripotency in mouse ES cells
Authors: Masui Shinji , Ohtsuka Satoshi , Yagi Rika , Takahashi Kadue , Ko Minoru SH , Niwa Hitoshi 
Published: April 2008

Abstract

Background

Rex1/Zfp42 has been extensively used as a marker for the undifferentiated state of pluripotent stem cells. However, its function in pluripotent stem cells including embryonic stem (ES) cells remained unclear although its involvement in visceral endoderm differentiation in F9 embryonal carcinoma (EC) cells was reported.

Results
We showed the function of Rex1 in mouse ES cells as well as in embryos using the conventional gene targeting strategy. Our results clearly indicated that Rex1 function is dispensable for both the maintenance of pluripotency in ES cells and the development of embryos. However, Rex1-/- ES cells showed the defect to induce a subset of the marker genes of visceral endoderm, when differentiated as embryoid body, as found in EC cells.

Conclusion

Rex1 should be regarded just as a marker of pluripotency without functional significance like the activity of alkaline phosphatase.
Transcriptomic changes induced by acute ozone in resistant and sensitive Medicago truncatulaaccessions
Authors: Puckette Michael C , Tang Yuhong , Mahalingam Ramamurthy 
Published: April 2008

AbstractBackgroundTropospheric ozone, the most abundant air pollutant is detrimental to plant and animal health including humans. In sensitive plant species even a few hours of exposure to this potent oxidant (200–300 nL. L-1) leads to severe oxidative stress that manifests as visible cell death. In resistant plants usually no visible symptoms are observed on exposure to similar ozone concentrations. Naturally occurring variability to acute ozone in plants provides a valuable resource for examining molecular basis of the differences in responses to ozone. From our earlier study inMedicago truncatula, we have identified cultivar Jemalong is ozone sensitive and PI 464815 (JE154) is an ozone-resistant accession. Analyses of transcriptome changes in ozone-sensitive and resistant accession will provide important clues for understanding the molecular changes governing the plant responses to ozone.ResultsAcute ozone treatment (300 nL L-1for six hours) led to a reactive oxygen species (ROS) burst in sensitive Jemalong six hours post-fumigation. In resistant JE154 increase in ROS levels was much reduced compared to Jemalong. Based on the results of ROS profiling, time points for microarray analysis were one hour into the ozone treatment, end of treatment and onset of an ozone-induced ROS burst at 12 hours. Replicated temporal transcriptome analysis in these two accessions using 17 K oligonucleotide arrays revealed more than 2000 genes were differentially expressed. Significantly enriched gene ontologies (GOs) were identified using the Cluster Enrichment analysis program. A striking finding was the alacrity of JE154 in altering its gene expression patterns in response to ozone, in stark contrast to delayed transcriptional response of Jemalong. GOs involved in signaling, hormonal pathways, antioxidants and secondary metabolism were altered in both accessions. However, the repertoire of genes responding in each of these categories was different between the two accessions. Real-time PCR analysis confirmed the differential expression patterns of a subset of these genes.ConclusionThis study provided a cogent view of the unique and shared transcriptional responses in an ozone-resistant and sensitive accession that exemplifies the complexity of oxidative signaling in plants. Based on this study, and supporting literature in Arabidopsis we speculate that plants sensitive to acute ozone are impaired in perception of the initial signals generated by the action of this oxidant. This in turn leads to a delayed transcriptional response in the ozone sensitive plants. In resistant plants rapid and sustained activation of several signaling pathways enables the deployment of multiple mechanisms for minimizing the toxicity effect of this reactive molecule.
Genome-wide linkage scan for colorectal cancer susceptibility genes supports linkage to chromosome 3q
Authors: Picelli Simone , Vandrovcova Jana , Jones Siân , Djureinovic Tatjana , Skoglund Johanna , Zhou Xiao-Lei , Velculescu Victor E , Vogelstein Bert , Lindblom Annika 
Published: April 2008

Abstract

Background
Colorectal cancer is one of the most common causes of cancer-related mortality. The disease is clinically and genetically heterogeneous though a strong hereditary component has been identified. However, only a small proportion of the inherited susceptibility can be ascribed to dominant syndromes, such as Hereditary Non-Polyposis Colorectal Cancer (HNPCC) or Familial Adenomatous Polyposis (FAP). In an attempt to identify novel colorectal cancer predisposing genes, we have performed a genome-wide linkage analysis in 30 Swedish non-FAP/non-HNPCC families with a strong family history of colorectal cancer.

Methods
Statistical analysis was performed using multipoint parametric and nonparametric linkage.

Results
Parametric analysis under the assumption of locus homogeneity excluded any common susceptibility regions harbouring a predisposing gene for colorectal cancer. However, several loci on chromosomes 2q, 3q, 6q, and 7q with suggestive linkage were detected in the parametric analysis under the assumption of locus heterogeneity as well as in the nonparametric analysis. Among these loci, the locus on chromosome 3q21.1-q26.2 was the most consistent finding providing positive results in both parametric and nonparametric analyses Heterogeneity LOD score (HLOD) = 1.90, alpha = 0.45, Non-Parametric LOD score (NPL) = 2.1).

Conclusion
The strongest evidence of linkage was seen for the region on chromosome 3. Interestingly, the same region has recently been reported as the most significant finding in a genome-wide analysis performed with SNP arrays; thus our results independently support the finding on chromosome 3q.
Quantifying hepatitis C transmission risk using a new weighted scoring system for the Blood-Borne Virus Transmission Risk Assessment Questionnaire (BBV-TRAQ): Applications for community-based HCV surveillance, education and prevention
Authors: Stoové Mark A , Fry Craig L , Lintzeris Nicholas 
Published: April 2008

Abstract

Background
The hepatitis C virus (HCV) is a major cause of drug-related morbidity and mortality, with incidence data implicating a wide range of HCV transmission risk practices. The Blood-Borne Virus Transmission Risk Assessment Questionnaire (BBV-TRAQ) is a content valid instrument that comprehensively assesses HCV risk practices. This study examines the properties of a new weighted BBV-TRAQ designed to quantify HCV transmission risk among injecting drug users (IDU).

Methods
Analyses of cross-sectional surveys of Australian IDU (N = 450) were used to generate normative data and explore the properties of a weighted BBV-TRAQ. Items weights were assigned according to expert key informant ratings of HCV risk practices performed during the development stages of the BBV-TRAQ. A range of item weights was tested and psychometric properties explored. A weighting scheme was recommended based on the plausibility of normative subscale data in relation to research evidence and the ability of BBV-TRAQ scores to discriminate between HCV positive and negative participants.

Results
While retaining the psychometric properties of the unweighted scale and demonstrating good internal reliability. By taking into account the relative transmission risk of a broad range of putative HCV practices, the weighted BBV-TRAQ produced promising predictive validity results among IDU based on self-report HCV status, particularly among young and less experienced injectors.

Conclusion
Brief, easy to administer and score, and inexpensive to apply, the utility of the BBV-TRAQ for community based education and prevention is enhanced by the application of item weights, potentially offering a valid surrogate measure for HCV infection among IDU.
Streamlining tasks and roles to expand treatment and care for HIV: randomised controlled trial protocol
Authors: Fairall Lara R , Bachmann Max O , Zwarenstein Merrick F , Lombard Carl J , Uebel Kerry , van Vuuren Cloete , Steyn Dewald , Boulle Andrew , Bateman Eric D 
Published: April 2008

Abstract

Background
A major barrier to accessing free government-provided antiretroviral treatment (ART) in South Africa is the shortage of suitably skilled health professionals. Current South African guidelines recommend that only doctors should prescribe ART, even though most primary care is provided by nurses. We have developed an effective method of educational outreach to primary care nurses in South Africa. Evidence is needed as to whether primary care nurses, with suitable training and managerial support, can initiate and continue to prescribe and monitor ART in the majority of ART-eligible adults.

Methods/design
This is a protocol for a pragmatic cluster randomised trial to evaluate the effectiveness of a complex intervention based on and supporting nurse-led antiretroviral treatment (ART) for South African patients with HIV/AIDS, compared to current practice in which doctors are responsible for initiating ART and continuing prescribing. We will randomly allocate 31 primary care clinics in the Free State province to nurse-led or doctor-led ART. Two groups of patients aged 16 years and over will be included: a) 7400 registering with the programme with CD4 counts of ≤ 350 cells/mL (mainly to evaluate treatment initiation) and b) 4900 already receiving ART (to evaluate ongoing treatment and monitoring). The primary outcomes will be time to death (in the first group) and viral suppression (in the second group). Patients' survival, viral load and health status indicators will be measured at least 6-monthly for at least one year and up to 2 years, using an existing province-wide clinical database linked to the national death register.

Trial registration
Controlled Clinical Trials ISRCTN46836853
An assessment of the quality of randomised controlled trials conducted in China
Authors: Zhang Dalu , Yin Peng , Freemantle Nick , Jordan Rachel , Zhong Nanshan , Cheng KK 
Published: April 2008

Abstract

Background
Despite the rapid increase in research in China, little is known about the quality of clinical trials conducted there.

Methods
A systematic review and critical appraisal of randomised controlled trials (RCTs) conducted in China and published in 2004 was undertaken to describe their characteristics, assess the quality of their reporting, and where possible, the quality of their conduct. Randomised controlled trials in all disease areas and types of interventions, which took place in China and included Chinese citizens were identified using PubMed and hand searching the Journal Series of the Chinese Medical Association. Quality was assessed against a subset of criteria adapted from the CONSORT statement.

Results

Three hundred and seven RCTs were included. One hundred and ninety-nine (64.8%) failed to report methods of randomization and 254 (82.4%) did not mention blinding of either participants or investigators. Reporting of baseline characteristics, primary outcome and length of follow-up was inadequate in a substantial proportion of studies. Fewer than 11% of RCTs mentioned ethical approval and only 18.0% adequately discussed informed consent. However, dropout rates were very favourable with nearly 44% of trials reporting a zero dropout rate.

Conclusion
Reporting of RCTs in China requires substantial improvement to meet the targets of the CONSORT statement. The conduct of Chinese RCTs cannot be directly inferred from the standard of reporting; however without good reporting the methods of the trials cannot be clearly ascertained.
The many faces of ubiquitinated histone H2A: insights from the DUBs
Authors: Vissers Joseph HA , Nicassio Francesco , van Lohuizen Maarten , Di Fiore Pier Paolo , Citterio Elisabetta 
Published: April 2008

Abstract
Monoubiquitination of H2A is a major histone modification in mammalian cells. Understanding how monoubiquitinated H2A (uH2A) regulates DNA-based processes in the context of chromatin is a challenging question. Work in the past years linked uH2A to transcriptional repression by the Polycomb group proteins of developmental regulators. Recently, a number of mammalian deubiquitinating enzymes (DUBs) that catalyze the removal of ubiquitin from H2A have been discovered. These studies provide convincing evidence that H2A deubiquitination is connected with gene activation. In addition, uH2A regulatory enzymes have crucial roles in the cellular response to DNA damage and in cell cycle progression. In this review we will discuss new insights into uH2A biology, with emphasis on the H2A DUBs.
Prolonged, granulocyte–macrophage colony-stimulating factor-dependent, neutrophil survival following rheumatoid synovial fibroblast activation by IL-17 and TNFalpha
Authors: Parsonage Greg , Filer Andrew , Bik Magdalena , Hardie Debbie , Lax Sian , Howlett Katherine , Church Leigh D , Raza Karim , Wong See-Heng , Trebilcock Emily , Scheel-Toellner Dagmar , Salmon Mike , Lord Janet M , Buckley Christopher D 
Published: April 2008

Abstract
Introduction
A surprising feature of the inflammatory infiltrate in rheumatoid arthritis is the accumulation of neutrophils within synovial fluid and at the pannus cartilage boundary. Recent findings suggest that a distinct subset of IL-17-secreting T-helper cells (TH17 cells) plays a key role in connecting the adaptive and innate arms of the immune response and in regulating neutrophil homeostasis. We therefore tested the hypothesis that synovial fibroblasts bridge the biological responses that connect TH17 cells to neutrophils by producing neutrophil survival factors following their activation with IL-17.

Methods
IL-17-expressing cells in the rheumatoid synovium, and IL-17-expressing cells in the peripheral blood, and synovial fluid were examined by confocal microscopy and flow cytometry, respectively. Peripheral blood neutrophils were cocultured either with rheumatoid arthritis synovial fibroblasts (RASF) or with conditioned medium from RASF that had been pre-exposed to recombinant human IL-17, TNFα or a combination of the two cytokines. Neutrophils were harvested and stained with the vital mitochondrial dye 3,3'-dihexyloxacarbocyanine iodide before being enumerated by flow cytometry.

Results
TH17-expressing CD4+ cells were found to accumulate within rheumatoid synovial tissue and in rheumatoid arthritis synovial fluid. RASF treated with IL-17 and TNFα (RASFIL-17/TNF) effectively doubled the functional lifespan of neutrophils in coculture. This was entirely due to soluble factors secreted from the fibroblasts. Specific depletion of granulocyte–macrophage colony-stimulating factor from RASFIL-17/TNF-conditioned medium demonstrated that this cytokine accounted for approximately one-half of the neutrophil survival activity. Inhibition of phosphatidylinositol-3-kinase and NF-κB pathways showed a requirement for both signalling pathways in RASFIL-17/TNF-mediated neutrophil rescue.

Conclusion
The increased number of neutrophils with an extended lifespan found in the rheumatoid synovial microenvironment is partly accounted for by IL-17 and TNFα activation of synovial fibroblasts. TH17-expressing T cells within the rheumatoid synovium are likely to contribute significantly to this effect.