bluuebunny/crossref_metadata_2025_split huggingface dataset:
Limited knowledge on progestogen‐only contraception and risk of venous thromboembolism
Authors: BERGENDAL ANNICA , ODLIND VIVECA , PERSSON INGEMAR , KIELER HELLE 
Published: January 2009

AbstractObjective. To assess the current knowledge concerning progestogen‐only contraception (POC) and risks of venous thromboembolism (VTE). Design and setting. Systematic review of the literature on observational and analytical studies reporting risk estimates for VTE in women exposed to POCs. Methods and main outcome measures. We performed a computerized literature search in the Pub Med, Embase, and the Cochrane Library for studies published between 1966 and February 13, 2008. Based on the evaluated studies we calculated an overall risk estimate for VTE in association with POC. Results. Four case‐control studies and one cohort study were included. Of the case‐control studies, three reported an increased risk and one a decreased risk of VTE. The cohort study found divergent results depending on the type of statistical analysis used. None of the results was statistically significant. The overall odds ratio for POC‐associated VTE in the four case‐control studies was 1.45 (95% CI = 0.92–2.26). Conclusions. The risk of VTE associated with use of POCs is poorly investigated. The slightly elevated overall risk estimate might suggest an association between POC and an increased risk for VTE. The results must, however, be interpreted with caution due to the possibility of residual confounding. Well‐designed studies with sufficient statistical power to evaluate risks of VTE with POC are warranted.
Pre‐pregnancy transabdominal cerclage
Authors: THUESEN LEA LANGHOFF , DINESS BIRGITTE RODE , LANGHOFF‐ROOS JENS 
Published: January 2009

AbstractA consecutive series of 45 women with one or more previous second trimester deliveries, who had a pre‐pregnancy transabdominal cerclage (TAC) from 1999 to July 2007, was followed until January 2008.Within the observation period 50 pregnancies occurred in 36 women. Seven resulted in first trimester abortions, none in second trimester abortions or deliveries, and six were on‐going pregnancies. In the remaining 37 pregnancies the fetal salvage rate was 100%, and cesarean section was performed after 34 weeks (mean 36+5 weeks) in 36 (97%) pregnancies. One woman had three successful pregnancies following the procedure. No serious complications were associated with the application of TAC. One woman had a hysterectomy following cesarean section.Pre‐pregnancy TAC is a procedure with few complications and excellent outcome. The method may be considered in women with a second trimester fetal loss, when cervical incompetence cannot be ruled out.
Evaluation of the Effectiveness of Common Hospital Hand Disinfectants Against Methicillin-ResistantStaphylococcus aureus,Glycopeptide-Intermediate S.aureus,and Heterogeneous Glycopeptide-IntermediateS. aureus
Authors: Wootton Mandy , Walsh Timothy R. , Davies Eleri M. , Howe Robin A. 
Published: January 2009

Background.The presence of methicillin-resistantStaphylococcus aureus(MRSA) and glycopeptide-intermediateS. aureus(GISA) in hospitals poses a significant challenge to hospital infection control teams. The use of disinfectants for both surface and hand cleaning is an essential part of the infection control measures.Objective.To evaluate the effectiveness of common hospital hand disinfectants against MRSA, GISA, and heterogeneous GISA (hGISA).Methods.For methicillin-susceptible S.aureus(MSSA), MRSA, GISA, and hGISA, the levels of susceptibility to hand disinfectants and their active ingredients were determined. Suspension tests were performed on commercial handwashing products.Results.Minimum inhibitory concentrations (MICs) of 2-propanol, Chlorhexidine, and hexachlorophene were similar for all phenotypes. The MICs of cetrimide and triclosan were higher for the MRSA, GISA, and hGISA strains than for the MSSA strain. The MICs for the chlorhexidine-containing agents Hibisol and Hibiscrub (AstraZeneca) and for the propanol-containing agent Sterillium (Medline) were 1-2-fold lower for the MSSA strains than for the MRSA, GISA, and hGISA strains. Suspension tests showed that the GISA and hGISA strains were less susceptible to the triclosan-containing agent Aquasept (SSL) than were the MRSA and MSSA strains, with resistance increasing with glycopeptide resistance. Products containing Betadine (Purdue) were more effective against the GISA and hGISA strains than against the MRSA and MSSA strains, especially after the strain was exposed to the product for 30 seconds.Conclusions.Using the EN 1040 standard criteria for the performance of disinfectants, we determined that all agents, except 50% Aquasept for hGISA and 0.33% hexachlorophene for GISA, performed effectively. However, the GISA and hGISA strains were less susceptible to triclosan-containing products, compared with the MRSA stains, but were more susceptible to products containing Betadine.
MOTIFATOR: detection and characterization of regulatory motifs using prokaryote transcriptome data
Authors: Blom Evert-Jan , Roerdink Jos B. T. M. , Kuipers Oscar P. , van Hijum Sacha A. F. T. 
Published: January 2009

Abstract
Summary: Unraveling regulatory mechanisms (e.g. identification of motifs in cis-regulatory regions) remains a major challenge in the analysis of transcriptome experiments. Existing applications identify putative motifs from gene lists obtained at rather arbitrary cutoff and require additional manual processing steps. Our standalone application MOTIFATOR identifies the most optimal parameters for motif discovery and creates an interactive visualization of the results. Discovered putative motifs are functionally characterized, thereby providing valuable insight in the biological processes that could be controlled by the motif.
Availability: MOTIFATOR is freely available at http://www.motifator.nl
Contact: o.p.kuipers@rug.nl; sacha.vanhijum@nizo.nl
AssociationViewer: a scalable and integrated software tool for visualization of large-scale variation data in genomic context
Authors: Martin Olivier , Valsesia Armand , Telenti Amalio , Xenarios Ioannis , Stevenson Brian J. 
Published: January 2009

Abstract
Summary: We present a tool designed for visualization of large-scale genetic and genomic data exemplified by results from genome-wide association studies. This software provides an integrated framework to facilitate the interpretation of SNP association studies in genomic context. Gene annotations can be retrieved from Ensembl, linkage disequilibrium data downloaded from HapMap and custom data imported in BED or WIG format. AssociationViewer integrates functionalities that enable the aggregation or intersection of data tracks. It implements an efficient cache system and allows the display of several, very large-scale genomic datasets.
Availability: The Java code for AssociationViewer is distributed under the GNU General Public Licence and has been tested on Microsoft Windows XP, MacOSX and GNU/Linux operating systems. It is available from the SourceForge repository. This also includes Java webstart, documentation and example datafiles.
Contact: brian.stevenson@licr.org
Supplementary information: Supplementary data are available at http://sourceforge.net/projects/associationview/ online.
Variable locus length in the human genome leads to ascertainment bias in functional inference for non-coding elements
Authors: Taher Leila , Ovcharenko Ivan 
Published: January 2009

Abstract
Motivation: Several functional gene annotation databases have been developed in the recent years, and are widely used to infer the biological function of gene sets, by scrutinizing the attributes that appear over- and underrepresented. However, this strategy is not directly applicable to the study of non-coding DNA, as the non-coding sequence span varies greatly among different gene loci in the human genome and longer loci have a higher likelihood of being selected purely by chance. Therefore, conclusions involving the function of non-coding elements that are drawn based on the annotation of neighboring genes are often biased. We assessed the systematic bias in several particular Gene Ontology (GO) categories using the standard hypergeometric test, by randomly sampling non-coding elements from the human genome and inferring their function based on the functional annotation of the closest genes. While no category is expected to occur significantly over- or underrepresented for a random selection of elements, categories such as ‘cell adhesion’, ‘nervous system development’ and ‘transcription factor activities’ appeared to be systematically overrepresented, while others such as ‘olfactory receptor activity’—underrepresented.
Results: Our results suggest that functional inference for non-coding elements using gene annotation databases requires a special correction. We introduce a set of correction coefficients for the probabilities of the GO categories that accounts for the variability in the length of the non-coding DNA across different loci and effectively eliminates the ascertainment bias from the functional characterization of non-coding elements. Our approach can be easily generalized to any other gene annotation database.
Contact: ovcharei@ncbi.nlm.nih.gov
Supplementary information: Supplementary data are available at Bioinformatics Online.
Predictors of fatal and non‐fatal outcomes in the Controlled Rosuvastatin Multinational Trial in Heart Failure (CORONA): incremental value of apolipoprotein A‐1, high‐sensitivity C‐reactive peptide and N‐terminal pro B‐type natriuretic peptide
Authors: Wedel Hans , McMurray John J.V. , Lindberg Magnus , Wikstrand John , Cleland John G.F. , Cornel Jan H. , Dunselman Peter , Hjalmarson Åke , Kjekshus John , Komajda Michel , Kuusi Timo , Vanhaecke Johan , Waagstein Finn ,   on behalf of the CORONA Study Group
Published: January 2009

AimsFew prognostic models in heart failure have been developed in typically elderly patients treated with modern pharmacological therapy and even fewer included simple biochemical tests (such as creatinine), new biomarkers (such as natriuretic peptides), or, especially, both. In addition, most models have been developed for the single outcome of all‐cause mortality.Methods and resultsWe built a series of models for nine different fatal and non‐fatal outcomes. For each outcome, a model was first built using demographic and clinical variables (Step 1), then with the addition of biochemical measures (serum creatinine, alanine aminotransferase, creatine kinase, thyrotrophin, apolipoproteins A‐1 and B, and triglycerides) (Step 2) and finally with the incorporation of high‐sensitivity C‐reactive protein (hsCRP) and N‐terminal pro B‐type natriuretic peptide (NT‐proBNP). Ranked according to the Wald χ2 value, age (56), ejection fraction (44), and body mass index (42) were most predictive of all‐cause mortality in Step 1 (total model χ2 343). Creatinine was the most powerful predictor at Step 2 (48) and ApoA‐1 ranked fifth (25), with the overall χ2 increasing to 440. Log NT‐proBNP (167) was the most powerful of the 14 independently predictive variables identified at Step 3 and the overall χ2 increased to 600. NT‐proBNP was the most powerful predictor of each other outcome. hsCRP was not a predictor of all‐cause mortality but did predict the composite atherothrombotic outcome.ConclusionOf the two new biomarkers studied in prognostic models in heart failure, NT‐proBNP, but not hsCRP, added substantial and independent predictive information, for a range of clinical outcomes, to that provided by simple demographic, clinical, and biochemical measures. ApoA‐1 was more predictive than LDL or HDL.
Inclusion of prey data improves prediction of bluefin tuna (Thunnus thynnus) distribution
Authors: SCHICK R. S. , LUTCAVAGE M. E. 
Published: January 2009

AbstractWe examined the distribution of Atlantic bluefin tuna (Thunnus thynnus) in the Gulf of Maine, Northwest Atlantic Ocean, from 17 to 23 August 1995, in relation to physical and biological parameters. Specifically, we fit a binomial GLM to the bluefin tuna presence–absence data and predictor variables that include: sea surface temperature (SST), ocean depth, distance to an SST front, time‐lagged density of SST fronts, and an interpolated surface of Atlantic herring (Clupea harengus) density. In addition, we use simple and partial Mantel tests to examine whether bluefin tuna presence–absence data are significantly associated with these predictors, once spatial autocorrelation is accounted for. Results suggest that the distribution of bluefin tuna significantly correlated with herring density (z = 3.525, P = 0.000424), and that inclusion of biological variables results in a more parsimonious model. Mantel tests results indicate that bluefin tuna abundance is significantly correlated with herring density after the effect of spatial structure is removed (Mantel r = 0.043, P < 0.019).
Importance of tumour cell invasion in blood and lymphatic vasculature among patients with endometrial carcinoma
Authors: Mannelqvist Monica , Stefansson Ingunn , Salvesen Helga B , Akslen Lars A 
Published: January 2009

Aims:  Vascular invasion is a prognostic marker for many cancers, including endometrial carcinoma. Immunohistochemistry using D2‐40 and CD31 antibodies makes it possible to differentiate between lymphatic vascular invasion (LVI) and blood vessel invasion (BVI). The aim was to examine lymphatic and blood vessel invasion separately and their associations with clinicopathological characteristics and prognosis.Methods and results:  Immunohistochemistry was performed on a retrospective population‐based series of endometrial carcinoma. Altogether, 31% of the 276 tumours showed lymphatic involvement, whereas 18% showed blood vessel invasion. LVI and BVI were associated with histopathological variables such as histological grade and tumour growth pattern. Patients without vascular invasion had the best prognosis and those with BVI (with or without LVI) had the worst outcome, whereas patients with LVI had an intermediate survival on univariate analysis. Multivariate models indicated that both LVI and especially BVI had independent prognostic importance. Among endometrioid carcinomas, BVI was still significant.Conclusions:  Our findings support the biological importance of vascular spread through the haematogenic and lymphatic routes in endometrial cancer. The significant correlation found with clinical phenotype indicates that these markers may be relevant for patient management.
A genetic network of flowering‐time genes in wheat leaves, in which an APETALA1/FRUITFULL‐like gene, VRN1, is upstream of FLOWERING LOCUS T
Authors: Shimada Sanae , Ogawa Taiichi , Kitagawa Satoshi , Suzuki Takayuki , Ikari Chihiro , Shitsukawa Naoki , Abe Tomoko , Kawahigashi Hiroyuki , Kikuchi Rie , Handa Hirokazu , Murai Koji 
Published: January 2009

SummaryTo elucidate the genetic mechanism of flowering in wheat, we performed expression, mutant and transgenic studies of flowering‐time genes. A diurnal expression analysis revealed that a flowering activator VRN1, an APETALA1/FRUITFULL homolog in wheat, was expressed in a rhythmic manner in leaves under both long‐day (LD) and short‐day (SD) conditions. Under LD conditions, the upregulation of VRN1 during the light period was followed by the accumulation of FLOWERING LOCUS T (FT) transcripts. Furthermore, FT was not expressed in a maintained vegetative phase (mvp) mutant of einkorn wheat (Triticum monococcum), which has null alleles of VRN1, and never transits from the vegetative to the reproductive phase. These results suggest that VRN1 is upstream of FT and upregulates the FT expression under LD conditions. The overexpression of FT in a transgenic bread wheat (Triticum aestivum) caused extremely early heading with the upregulation of VRN1 and the downregulation of VRN2, a putative repressor gene of VRN1. These results suggest that in the transgenic plant, FT suppresses VRN2 expression, leading to an increase in VRN1 expression. Based on these results, we present a model for a genetic network of flowering‐time genes in wheat leaves, in which VRN1 is upstream of FT with a positive feedback loop through VRN2. The mvp mutant has a null allele of VRN2, as well as of VRN1, because it was obtained from a spring einkorn wheat strain lacking VRN2. The fact that FT is not expressed in the mvp mutant supports the present model.
Shoot apical meristem function in Arabidopsis requires the combined activities of three BEL1‐like homeodomain proteins
Authors: Rutjens Bas , Bao Dongping , Van Eck‐Stouten Evelien , Brand Marco , Smeekens Sjef , Proveniers Marcel 
Published: January 2009

SummaryIn plants, most of the above‐ground body is formed post‐embryonically by the continuous organogenic potential of the shoot apical meristem (SAM). Proper function of the SAM requires maintenance of a delicate balance between the depletion of stem cell daughters into developing primordia and proliferation of the central stem cell population. Here we show that initiation and maintenance of the Arabidopsis SAM, including that of floral meristems, requires the combinatorial action of three members of the BELL‐family of TALE homeodomain proteins, ARABIDOPSIS THALIANA HOMEOBOX 1 (ATH1), PENNYWISE (PNY) and POUND‐FOOLISH (PNF). All three proteins interact with the KNOX TALE homeodomain protein STM, and combined lesions in ATH1, PNY and PNF result in a phenocopy of stm mutations. Therefore, we propose that ath1 pny pnf meristem defects result from loss of combinatorial BELL‐STM control. Further, we demonstrate that heterodimerization‐controlled cellular localization of BELL and KNOX proteins involves a CRM1/exportin‐1‐mediated nuclear exclusion mechanism that is probably generic to control the activity of BELL and KNOX combinations. We conclude that in animals and plants corresponding mechanisms regulate the activity of TALE homeodomain proteins through controlled nuclear‐cytosolic distribution of these proteins.
Calcium depletion and calmodulin inhibition affect the import of nuclear‐encoded proteins into plant mitochondria
Authors: Kuhn Sabine , Bussemer Johanna , Chigri Fatima , Vothknecht Ute C. 
Published: January 2009

SummaryMany metabolic processes essential for plant viability take place in mitochondria. Therefore, mitochondrial function has to be carefully balanced in accordance with the developmental stage and metabolic requirements of the cell. One way to adapt organellar function is the alteration of protein composition. Since most mitochondrial proteins are nuclear encoded, fine‐tuning of mitochondrial protein content could be achieved by the regulation of protein translocation. Here we present evidence that the import of nuclear‐encoded mitochondrial proteins into plant mitochondria is influenced by calcium and calmodulin. In pea mitochondria, the calmodulin inhibitor ophiobolin A as well as the calcium ionophores A23187 and ionomycin inhibit translocation of nuclear‐encoded proteins in a concentration‐dependent manner, an effect that can be countered by the addition of external calmodulin or calcium, respectively. Inhibition was observed exclusively for proteins translocating into or across the inner membrane but not for proteins residing in the outer membrane or the intermembrane space. Ophiobolin A and the calcium ionophores further inhibit translocation into mitochondria with disrupted outer membranes, but their effect is not mediated via a change in the membrane potential across the inner mitochondrial membrane. Together, our results suggest that calcium/calmodulin influences the import of a subset of mitochondrial proteins at the inner membrane. Interestingly, we could not observe any influence of ophiobolin A or the calcium ionophores on protein translocation into mitochondria of yeast, indicating that the effect of calcium/calmodulin on mitochondrial protein import might be a plant‐specific trait.
Impact of allergic rhinitis on asthma: effects on bronchial hyperreactivity
Authors: Cirillo I. , Pistorio A. , Tosca M. , Ciprandi G. 
Published: January 2009

Background:  Remarkable relationship exists between upper and lower airways. Bronchial hyperreactivity (BHR) is a paramount feature of asthma and may be considered a strong risk factor for the onset of asthma in patients with allergic rhinitis.Objective:  This study is aimed at evaluating the presence of BHR in a large group of patients with moderate‐severe persistent allergic rhinitis alone, and at investigating possible risk factors related to severe BHR.Methods:  Three hundred and forty‐two patients with moderate‐severe persistent allergic rhinitis were prospectively and consecutively evaluated. Clinical examination, skin prick test, spirometry and bronchial methacholine (MCH) test were performed in all patients.Results:  Twenty‐two (6.4%) patients had severe BHR, 74 (21.6%) patients had mild BHR and 192 (56.2%) had borderline BHR; 54 (15.8%) patients had a negative MCH test. The logistic regression analysis evidenced that trees and house dust mites sensitization (ORAdj: 8.1), rhinitis duration > 5 years (ORAdj: 5.4) and FEV1 ≤ 86% of predicted (ORAdj: 4.0) were significantly associated with severe BHR. The discriminative ability of this model is appreciably satisfactory, being the AUC = 0.90.Conclusion:  This study highlights the close link between upper and lower airways and the role of some risk factors, such as tree and mite sensitization, > 5‐year duration, and ≤ 86% FEV1 values, as risk factors for severe BHR in patients with moderate‐severe persistent allergic rhinitis alone. Therefore, BHR is frequently present in patients with chronic rhinitis and should be suspected in the presence of defined risk factors.
Comparative enzymology of native and recombinant house dust mite allergen Der p 1
Authors: Zhang J. , Saint‐Remy J.‐M. , Garrod D. R. , Robinson C. 
Published: January 2009

Background:  The cysteine peptidase activity of group 1 house dust mite allergens is important for their allergenicity and may offer new therapeutic targets for allergy treatment. Hitherto, the design of specific inhibitors has been impeded because the availability of pure, fully active allergens has limited the implementation of drug screening campaigns. Similarly, investigation of the mechanisms by which peptidase allergens promote sensitization has also been restricted. Our aim was to compare the enzymology of recombinant and native forms of Der p 1 to establish if an easily expressed recombinant form of Der p 1 could be used as a drug discovery tool.Methods:  Enzymatic activity of natural and recombinant Der p 1 was compared fluorimetrically using a novel specific substrate (ADZ 50,059) and a novel specific active site titrant (ADZ 50,000). The effect of recombinant Der p 1 prodomain on the catalytic activity of both Der p 1 preparations was also examined.Results:  Although differing substantially in molecular weight, the enzymological properties of recombinant and native Der p 1 were indistinguishable. Our data show clearly by experiment that, in contrast to some suggestions, Der p 1 is not an enzyme of bifunctional mechanism.Conclusion:  The catalytic activity of Der p 1 is tolerant of glycosylation differences that occur at N150 when the protein is expressed in Pichia pastoris. This suggests that this recombinant protein may be suitable for drug design studies and in the elucidation of how peptidase activity promotes sensitization to peptidase and nonpeptidase bystander allergens.