bluuebunny/crossref_metadata_2025_split huggingface dataset:
Active or passive bio-coating: does it matters in extracorporeal circulation?
Authors: Jacobs S , De Somer F , Vandenplas G , Van Belleghem Y , Taeymans Y , Van Nooten G 
Published: July 2011

Background: Two types of surface coating for cardiopulmonary bypass (CPB) are used: bioactive (heparin, nitric oxide) and biopassive (albumin, polyethyleneoxide (PEO), phosphorylcholine). When haemocompatible coatings are combined with the separation of pleuro-pericardial aspiration, attenuation of both the coagulation and complement cascades, as well as better platelet preservation, has been demonstrated. This study wants to investigate if the combination of a bioactive with a biopassive coating (unfractionated heparin embedded in a phosphorylcholine matrix) combines the beneficial effects of both approaches. Materials and methods: Thirty patients undergoing elective CABG were prospectively randomized into two groups of 15 patients. The sole exclusion criterion was an ejection fraction of less than 40%. In the control group (PC), the whole CPB circuit was coated with phosphorylcholine (PC). In the study group (XPC), unfractionated heparin was embedded in the PC matrix of the oxygenator and arterial line filter. Results: No differences were found for haemolytic index, thrombin-anti-thrombin complex (TAT), IL-6, IL-10 and blood loss. PF4 plasma concentration increased from 27.6±22.0 IU/mL to 165.7±43.9 IU/mL (p<0.001) at 15 minutes of CPB in the PC and from 16.0±9.7 IU/mL to 150.9 ± 61.3 IU/mL (p<0.001) in the XPC group. Terminal complement complex (TCC) increased over time in both groups until the end of CPB (Figure 2A). Within each group, TCC generation was statistically significantly higher after the release of the aortic cross-clamp (p<0.001) and at the end of CPB (p<0.001). Total TCC generation was statistically significantly higher in the XPC group compared to the PC group (p=0.026). The difference was statistically significant after the release of the aortic cross-clamp (p=0.005) and at the end of CPB (p=0.001). Conclusions: Based on our results, there is no additional benefit in combining phosphorylcholine with unfractionated heparin in elective patients undergoing coronary artery bypass grafting (CABG). Massive haemodilution leads to enhanced complement activation.
Age- and gender-related long-term renal outcome in patients with lupus nephritis
Authors: Hsu C-Y , Chiu W-C , Yang T-S , Chen C-J , Chen Y-C , Lai H-M , Yu S-F , Su Y-J , Cheng T-T 
Published: July 2011

Objective: To investigate age- and gender-related long-term renal outcome in patients with lupus nephritis (LN). Methods: This is a retrospective, chart review study of patients with LN at Chang Gung Memorial Hospital, Kaohsiung, between January 1986 and June 2004. All had undergone a renal biopsy that showed LN. The end point of outcome was chronic renal insufficiency (CRI), which was defined as ‘doubling of baseline serum creatinine lasting for at least 6 months with a value at least 2 mg/dl.’ The patients were categorized by age tertiles and gender. A 5-year survival curve was constructed to study the effect of age and gender on the outcome. Results: In total, 121 sets of patient data were evaluated. The study group included 104 women and 17 men. Of the study patients, 26 (21%) developed CRI after 5 years of follow-up. There was no significant difference among age groups in developing CRI ( p = 0.23). In terms of gender, men had worse long-term renal outcome ( p = 0.004) than women. Conclusions: The long-term renal outcome of the LN patients did not differ among age groups, but was worse in men.
Maintenance best practice and recent research
Authors: Fleming P 
Published: July 2011

This paper sets out to capture the recent discussions on maintenance ‘best practice’ for artificial turf surfaces and some related research. The information presented comes partly from a seminar in 2009, providing a mix of quantitative and qualitative information and opinions from a range of contributors both academic and industrial organized by the research network SportSURF (based at Loughborough University), and is supplemented with a case study of practices at Loughborough University on three different outdoor synthetic surfaces. The best practice information is further enhanced with recent research findings from a study investigating damage to artificial carpet fibres caused by power brushing. The outcomes of the maintenance seminar showed a good consensus for aspects of the most relevant type and frequency of maintenance tasks, with a useful rule of thumb for pitch managers of one hour of maintenance for every 10 hours of use of the surface system. Maintenance costs for artificial turf has traditionally been marketed as being ‘low’, but the data show costs per annum should be expected to be similar to natural turf but when expressed as a cost ‘per hour of use’ then the relative cost to be much lower for artificial turf than natural turf. Damage caused by power brushing, from a short laboratory study, was found to be minimal in terms of fibre splits or breaks for three (standard) brush systems of varying stiffness and for three different carpet systems (both sand and rubber infill systems). This paper collectively provides an advance in the knowledge and debate for the specialist practice of artificial surface maintenance, currently under-researched and poorly disseminated.
Type I-IFNs control GVHD and GVL responses after transplantation
Authors: Robb Renee J. , Kreijveld Ellen , Kuns Rachel D. , Wilson Yana A. , Olver Stuart D. , Don Alistair L. J. , Raffelt Neil C. , De Weerd Nicole A. , Lineburg Katie E. , Varelias Antiopi , Markey Kate A. , Koyama Motoko , Clouston Andrew D. , Hertzog Paul J. , MacDonald Kelli P. A. , Hill Geoffrey R. 
Published: July 2011

Abstract
Although the effects of type II-IFN (IFN-γ) on GVHD and leukemia relapse are well studied, the effects of type I-interferon (type I-IFN, IFN-α/β) remain unclear. We investigated this using type I-IFN receptor-deficient mice and exogenous IFN-α administration in established models of GVHD and GVL. Type I-IFN signaling in host tissue prevented severe colon-targeted GVHD in CD4-dependent models of GVHD directed toward either major histocompatibility antigens or multiple minor histocompatibility antigens. This protection was the result of suppression of donor CD4+ T-cell proliferation and differentiation. Studies in chimeric recipients demonstrated this was due to type I-IFN signaling in hematopoietic tissue. Consistent with this finding, administration of IFN-α during conditioning inhibited donor CD4+ proliferation and differentiation. In contrast, CD8-dependent GVHD and GVL effects were enhanced when type I-IFN signaling was intact in the host or donor, respectively. This finding reflected the ability of type I-IFN to both sensitize host target tissue/leukemia to cell-mediated cytotoxicity and augment donor CTL function. These data confirm that type I-IFN plays an important role in defining the balance of GVHD and GVL responses and suggests that administration of the cytokine after BM transplantation could be studied prospectively in patients at high risk of relapse.
Late MRD response determines relapse risk overall and in subsets of childhood T-cell ALL: results of the AIEOP-BFM-ALL 2000 study
Authors: Schrappe Martin , Valsecchi Maria Grazia , Bartram Claus R. , Schrauder André , Panzer-Grümayer Renate , Möricke Anja , Parasole Rosanna , Zimmermann Martin , Dworzak Michael , Buldini Barbara , Reiter Alfred , Basso Giuseppe , Klingebiel Thomas , Messina Chiara , Ratei Richard , Cazzaniga Giovanni , Koehler Rolf , Locatelli Franco , Schäfer Beat W. , Aricò Maurizio , Welte Karl , van Dongen Jacques J.M. , Gadner Helmut , Biondi Andrea , Conter Valentino 
Published: July 2011

Abstract
The prognostic value of MRD in large series of childhood T-ALL has not yet been established. Trial AIEOP-BFM-ALL 2000 introduced standardized quantitative assessment of MRD for stratification, based on immunoglobulin and TCR gene rearrangements as polymerase chain reaction targets: Patients were considered MRD standard risk (MRD-SR) if MRD was negative at day 33 (time point 1 [TP1]) and day 78 (TP2), analyzed by at least 2 sensitive markers; MRD intermediate risk (MRD-IR) if positive either at day 33 or 78 and < 10−3 at day 78; and MRD high risk (MRD-HR) if ≥ 10−3 at day 78. A total of 464 patients with T-ALL were stratified by MRD: 16% of them were MRD-SR, 63% MRD-IR, and 21% MRD-HR. Their 7-year event-free-survival (SE) was 91.1% (3.5%), 80.6% (2.3%), and 49.8% (5.1%) (P < .001), respectively. Negativity of MRD at TP1 was the most favorable prognostic factor. An excellent outcome was also obtained in 32% of patients turning MRD negative only at TP2, indicating that early (TP1) MRD levels were irrelevant if MRD at TP2 was negative (48% of all patients). MRD ≥ 10−3 at TP2 constitutes the most important predictive factor for relapse in childhood T-ALL. The study is registered at http://www.clinicaltrials.gov; “Combination Chemotherapy Based on Risk of Relapse in Treating Young Patients With Acute Lymphoblastic Leukemia,” protocol identification #NCT00430118 for BFM and #NCT00613457 for AIEOP.
Soluble IL-2Rα facilitates IL-2–mediated immune responses and predicts reduced survival in follicular B-cell non-Hodgkin lymphoma
Authors: Yang Zhi-Zhang , Grote Deanna M. , Ziesmer Steven C. , Manske Michelle K. , Witzig Thomas E. , Novak Anne J. , Ansell Stephen M. 
Published: July 2011

AbstractElevated serum levels of the soluble form of IL-2 receptor α (sIL-2Rα) have been correlated with a poor prognosis in a variety of different types of cancers. However, its biologic relevance remains unclear and controversial. In patients with follicular B-cell non-Hodgkin lymphoma (FL), we observed that serum sIL-2Rα levels were elevated compared with controls and that elevated sIL-2Rα levels before treatment were associated with a poor outcome. To explore the mechanism by which sIL-2Rα may contribute to a poor prognosis in FL, we determined the effects of sIL-2Rα on IL-2 signaling and found that the sIL-2Rα–IL-2 complex promoted T-cell differentiation toward to inhibitory Treg cells rather than TH1 or TH17 cells. Shed by activated T cells that express membrane-bound IL-2Rα, sIL-2Rα further enhanced IL-2–mediated phosphorylation of Stat5 thereby significantly up-regulating Foxp3 expression in CD4+ T cells. We found that CD4+ T cells treated with either IL-2 or sIL-2Rα–IL-2 complex, but not with sIL-2Rα alone, inhibited the function of CD8+ T cells. Taken together, these results indicate that sIL-2Rα actually plays an active biologic role in FL by binding IL-2 and promoting IL-2 signaling rather than depleting IL-2 and blocking its function.
Effects of granulocyte-colony stimulating factor on chromosome aneuploidy and replication asynchrony in healthy peripheral blood stem cell donors
Authors: Hirsch Betsy , Oseth LeAnn , Cain Meghan , Trader Erin , Pulkrabek Shelley , Lindgren Bruce , Luo Xianghua , Clay Mary , Miller John , Confer Dennis , Weisdorf Daniel , McCullough Jeffrey 
Published: July 2011

Abstract
As peripheral blood has surpassed bone marrow as a predominant source of stem cells for transplantation, use of the cytokine granulocyte colony-stimulating factor (G-CSF) to mobilize peripheral blood stem cells (PBSCs) is increasing. Issues regarding potential genotoxic effects of even short-term, low-dose G-CSF treatment for the healthy donors have been raised. To address the question of chromosomal instability, we used FISH to evaluate the peripheral blood lymphocytes of 22 PBSC donors and 22 matched controls at 5 time points over a 12-month period. The specimens obtained were a pre-G-CSF, followed by collections at the time of PBSC harvest (days 5-7) and at 2, 6, and 12 months after donation. Eight additional PBSC donors provided a single sample at 12 months. Nine loci (mapped to chromosomes 7, 8, 9, 17, 21, and 22) were evaluated for aneuploidy, including 3 mapped to chromosome 7 because of the specific relevance of monosomy 7. Replication timing was evaluated for chromosome 15 and 17 loci. No evidence was found of G-CSF–induced chromosomal instability. This work supports the epidemiologic data that have demonstrated no increased risk for hematologic malignancies in G-CSF–primed PBSC donors.
Airflow limitation, lung volumes and systemic inflammation in a general population
Authors: Gläser S. , Ittermann T. , Koch B. , Völzke H. , Wallaschofski H. , Nauck M. , Warnke C. , Vogelmeier C. , Schulz H. , Felix S.B. , Ewert R. , Schäper C. 
Published: July 2011

Although several levels of evidence have suggested an association between systemic inflammation and spirometric lung volumes, data addressing the potential interrelationship between airflow limitation and inflammatory markers are sparse and remain controversial.Potential associations between high-sensitivity C-reactive protein (hsCRP), fibrinogen and lung function were investigated in 1,466 individuals aged 25–85 yrs, representing a general population. Within this cross-sectional population, data on body plethysmography, spirometry, helium dilution and diffusing capacity of the lung for carbon monoxide (DL,CO) were analysed.After adjustment for potential confounding factors, such as smoking, obesity and cardiorespiratory fitness, there was an inverse association of hsCRP with forced expiratory and static lung volumes. In neither apparently healthy nor the entire population was inflammation associated with airflow limitation in central airways. In smokers only, higher hsCRP and fibrinogen were associated with an impairedDL,CO.This study shows that higher levels of hsCRP are associated with decreased lung volumes in a general population over a wide age range. A consistent interrelationship of central airflow limitation and inflammation was not verifiable. Smoking is related to an impairedDL,COin association with an increase in systemic inflammation.
Rehabilitation and acute exacerbations
Authors: Burtin C. , Decramer M. , Gosselink R. , Janssens W. , Troosters T. 
Published: July 2011

Recent evidence indicates that acute exacerbations of chronic obstructive pulmonary disease aggravate the extrapulmonary consequences of the disease. Skeletal muscle dysfunction, a sustained decrease in exercise tolerance, enhanced symptoms of depression and fatigue are reported. Avoidance of physical activities is likely to be a key underlying mechanism and increases the risk of new exacerbations. Pulmonary rehabilitation is an intervention targeting these systemic consequences. Exercise strategies need to be adapted to the increased feelings of dyspnoea and fatigue.This review aims to describe the systemic consequences of acute exacerbations and compiles evidence for the feasibility and effectiveness of different rehabilitation strategies to counteract these consequences during and/or immediately after the acute phase of the exacerbation. Resistance training and neuromuscular electrical stimulation have been applied safely in frail, hospitalised patients and have the potential to prevent muscle atrophy. Comprehensive pulmonary rehabilitation, including general exercise training, can be implemented immediately after the exacerbation, leading to a reduction in hospital admissions and an increase in exercise tolerance and quality of life. Self-management strategies play a crucial role in changing disease-related health behaviour and preventing hospital admissions.
DNACLUST: accurate and efficient clustering of phylogenetic marker genes
Authors: Ghodsi Mohammadreza , Liu Bo , Pop Mihai 
Published: July 2011

Abstract

Background
Clustering is a fundamental operation in the analysis of biological sequence data. New DNA sequencing technologies have dramatically increased the rate at which we can generate data, resulting in datasets that cannot be efficiently analyzed by traditional clustering methods.
This is particularly true in the context of taxonomic profiling of microbial communities through direct sequencing of phylogenetic markers (e.g. 16S rRNA) - the domain that motivated the work described in this paper. Many analysis approaches rely on an initial clustering step aimed at identifying sequences that belong to the same operational taxonomic unit (OTU). When defining OTUs (which have no universally accepted definition), scientists must balance a trade-off between computational efficiency and biological accuracy, as accurately estimating an environment's phylogenetic composition requires computationally-intensive analyses. We propose that efficient and mathematically well defined clustering methods can benefit existing taxonomic profiling approaches in two ways: (i) the resulting clusters can be substituted for OTUs in certain applications; and (ii) the clustering effectively reduces the size of the data-sets that need to be analyzed by complex phylogenetic pipelines (e.g., only one sequence per cluster needs to be provided to downstream analyses).

Results
To address the challenges outlined above, we developed DNACLUST, a fast clustering tool specifically designed for clustering highly-similar DNA sequences.
Given a set of sequences and a sequence similarity threshold, DNACLUST creates clusters whose radius is guaranteed not to exceed the specified threshold. Underlying DNACLUST is a greedy clustering strategy that owes its performance to novel sequence alignment and k- mer based filtering algorithms.
DNACLUST can also produce multiple sequence alignments for every cluster, allowing users to manually inspect clustering results, and enabling more detailed analyses of the clustered data.

Conclusions
We compare DNACLUST to two popular clustering tools: CD-HIT and UCLUST. We show that DNACLUST is about an order of magnitude faster than CD-HIT and UCLUST (exact mode) and comparable in speed to UCLUST (approximate mode). The performance of DNACLUST improves as the similarity threshold is increased (tight clusters) making it well suited for rapidly removing duplicates and near-duplicates from a dataset, thereby reducing the size of the data being analyzed through more elaborate approaches.
InterMitoBase: An annotated database and analysis platform of protein-protein interactions for human mitochondria
Authors: Gu Zuguang , Li Jie , Gao Song , Gong Ming , Wang Junling , Xu Hua , Zhang Chenyu , Wang Jin 
Published: July 2011

Abstract

Background
The mitochondrion is an essential organelle which plays important roles in diverse biological processes, such as metabolism, apoptosis, signal transduction and cell cycle. Characterizing protein-protein interactions (PPIs) that execute mitochondrial functions is fundamental in understanding the mechanisms underlying biological functions and diseases associated with mitochondria. Investigations examining mitochondria are expanding to the system level because of the accumulation of mitochondrial proteomes and human interactome. Consequently, the development of a database that provides the entire protein interaction map of the human mitochondrion is urgently required.

Results
InterMitoBase provides a comprehensive interactome of human mitochondria. It contains the PPIs in biological pathways mediated by mitochondrial proteins, the PPIs between mitochondrial proteins and non-mitochondrial proteins as well as the PPIs between mitochondrial proteins. The current version of InterMitoBase covers 5,883 non-redundant PPIs of 2,813 proteins integrated from a wide range of resources including PubMed, KEGG, BioGRID, HPRD, DIP and IntAct. Comprehensive curations have been made on the interactions derived from PubMed. All the interactions in InterMitoBase are annotated according to the information collected from their original sources, GenBank and GO. Additionally, InterMitoBase features a user-friendly graphic visualization platform to present functional and topological analysis of PPI networks identified. This should aid researchers in the study of underlying biological properties.

Conclusions
InterMitoBase is designed as an integrated PPI database which provides the most up-to-date PPI information for human mitochondria. It also works as a platform by integrating several on-line tools for the PPI analysis. As an analysis platform and as a PPI database, InterMitoBase will be an important database for the study of mitochondria biochemistry, and should be particularly helpful in comprehensive analyses of complex biological mechanisms underlying mitochondrial functions.
Genome-wide expression quantitative trait loci (eQTL) analysis in maize
Authors: Holloway Beth , Luck Stanley , Beatty Mary , Rafalski J-Antoni , Li Bailin 
Published: July 2011

Abstract

Background
Expression QTL analyses have shed light on transcriptional regulation in numerous species of plants, animals, and yeasts. These microarray-based analyses identify regulators of gene expression as either cis-acting factors that regulate proximal genes, or trans-acting factors that function through a variety of mechanisms to affect transcript abundance of unlinked genes.

Results
A hydroponics-based genetical genomics study in roots of a Zea mays IBM2 Syn10 double haploid population identified tens of thousands of cis-acting and trans-acting eQTL. Cases of false-positive eQTL, which results from the lack of complete genomic sequences from both parental genomes, were described. A candidate gene for a trans-acting regulatory factor was identified through positional cloning. The unexpected regulatory function of a class I glutamine amidotransferase controls the expression of an ABA 8'-hydroxylase pseudogene.

Conclusions
Identification of a candidate gene underlying a trans-eQTL demonstrated the feasibility of eQTL cloning in maize and could help to understand the mechanism of gene expression regulation. Lack of complete genome sequences from both parents could cause the identification of false-positive cis- and trans-acting eQTL.
Identification and characterization of microRNAs from Phaeodactylum tricornutum by high-throughput sequencing and bioinformatics analysis
Authors: Huang Aiyou , He Linwen , Wang Guangce 
Published: July 2011

Abstract

Background
Diatoms, which are important planktons widespread in various aquatic environments, are believed to play a vital role in primary production as well as silica cycling. The genomes of the pennate diatom Phaeodactylum tricornutum and the centric diatom Thalassiosira pseudonana have been sequenced, revealing some characteristics of the diatoms' mosaic genome as well as some features of their fatty acid metabolism and urea cycle, and indicating their unusual properties. To identify microRNAs (miRNAs) from P. tricornutum and to study their probable roles in nitrogen and silicon metabolism, we constructed and sequenced small RNA (sRNA) libraries from P. tricornutum under normal (PT1), nitrogen-limited (PT2) and silicon-limited (PT3) conditions.

Results
A total of 13 miRNAs were identified. They were probable P. tricornutum-specific novel miRNAs. These miRNAs were sequenced from P. tricornutum under normal, nitrogen-limited and/or silicon-limited conditions, and their potential targets were involved in various processes, such as signal transduction, protein amino acid phosphorylation, fatty acid biosynthetic process, regulation of transcription and so on.

Conclusions
Our results indicated that P. tricornutum contained novel miRNAs that have no identifiable homologs in other organisms and that they might play important regulator roles in P. tricornutum metabolism.