bluuebunny/crossref_metadata_2025_split huggingface dataset:
Risk of Vancomycin-ResistantEnterococcus(VRE) Bloodstream Infection Among Patients Colonized With VRE
Authors: Olivier Chamion N. , Blake Ruth K. , Steed Lisa L. , Salgado Cassandra D. 
Published: April 2008

Background.Colonization with vancomycin-resistantEnterococcus(VRE) is a risk factor for subsequent VRE bloodstream infection (BSI); however, risk factors for BSI among colonized patients have not been adequately described. We sought to determine the proportion of VRE-colonized patients who subsequently develop VRE BSI and to identify risk factors for VRE BSI among these patients.Methods.Records of 768 patients colonized with VRE from January 2002 through June 2005 were reviewed. The proportion of patients who developed VRE BSI was calculated, and the characteristics of these patients were compared, in a 2 : 1 ratio, with those of patients who did not develop VRE BSI. To identify risk factors for VRE BSI and for death, we used univariate logistic regression analysis and then multivariate logistic regression analysis. Using pulsed-field gel electrophoresis (PFGE), we compared the isolate recovered when the patient was colonized and the isolate recovered when the patient developed VRE BSI.Results.Of the 768 patients colonized with VRE, 31 (4.0%) developed VRE BSI. Multivariate analysis identified the following idependent risk factors for developing VRE BSI: infection of an additional body site other than blood (adjusted odds ratio [aOR], 3.9;P= .04), admission to the hospital from a long-term care facility (aOR, 12.6;P= .04), and receipt of vancomycin (aOR, 10.6;P< .001). The independent risk factors for death among patients colonized with VRE were immunosuppression (aOR, 12.9;P= .001 ) and VRE BSI (aOR, 9.1;P= .002). Of the 31 patients who developed VRE BSI, 23 (74%) had a pair of isolates representing VRE colonization and VRE BSI. For 19 (83%) of these 23 patients, the isolate representing BSI was genetically related to the isolate representing VRE colonization: 12 pairs of isolates (52%) had identical banding patterns, 5 had closely related patterns, and 2 had possibly related patterns.Conclusion.Of the 768 patients colonized with VRE, 31 (4.0%) usually developed VRE BSI due to a related strain. Independent risk factors for BSI among colonized patients were admission from a long-term care facility, infection of an additional body site, and exposure to vancomycin. Independent risk factors for death were immunosuppression and VRE BSI.
CompariMotif: quick and easy comparisons of sequence motifs
Authors: Edwards Richard J. , Davey Norman E. , Shields Denis C. 
Published: March 2008

Abstract
Summary: CompariMotif is a novel tool for making motif–motif comparisons, identifying and describing similarities between regular expression motifs. CompariMotif can identify a number of different relationships between motifs, including exact matches, variants of degenerate motifs and complex overlapping motifs. Motif relationships are scored using shared information content, allowing the best matches to be easily identified in large comparisons. Many input and search options are available, enabling a list of motifs to be compared to itself (to identify recurring motifs) or to datasets of known motifs.
Availability: CompariMotif can be run online at http://bioware.ucd.ie/ and is freely available for academic use as a set of open source Python modules under a GNU General Public License from http://bioinformatics.ucd.ie/shields/software/comparimotif/
Contact: r.edwards@southampton.ac.uk
Supplementary information: Further details are available at http://bioinformatics.ucd.ie/shields/software/comparimotif/
Analysis of correlated mutations in HIV-1 protease using spectral clustering
Authors: Liu Ying , Eyal Eran , Bahar Ivet 
Published: March 2008

Abstract
Motivation: The ability of human immunodeficiency virus-1 (HIV-1) protease to develop mutations that confer multi-drug resistance (MDR) has been a major obstacle in designing rational therapies against HIV. Resistance is usually imparted by a cooperative mechanism that can be elucidated by a covariance analysis of sequence data. Identification of such correlated substitutions of amino acids may be obscured by evolutionary noise.
Results: HIV-1 protease sequences from patients subjected to different specific treatments (set 1), and from untreated patients (set 2) were subjected to sequence covariance analysis by evaluating the mutual information (MI) between all residue pairs. Spectral clustering of the resulting covariance matrices disclosed two distinctive clusters of correlated residues: the first, observed in set 1 but absent in set 2, contained residues involved in MDR acquisition; and the second, included those residues differentiated in the various HIV-1 protease subtypes, shortly referred to as the phylogenetic cluster. The MDR cluster occupies sites close to the central symmetry axis of the enzyme, which overlap with the global hinge region identified from coarse-grained normal-mode analysis of the enzyme structure. The phylogenetic cluster, on the other hand, occupies solvent-exposed and highly mobile regions. This study demonstrates (i) the possibility of distinguishing between the correlated substitutions resulting from neutral mutations and those induced by MDR upon appropriate clustering analysis of sequence covariance data and (ii) a connection between global dynamics and functional substitution of amino acids.
Contact: bahar@ccbb.pitt.edu
Supplementary information: Supplementary data are available at Bioinformatics online.
Developing a beam trawl for sampling estuarine fish and crustaceans: assessment of a codend cover and effects of different sizes of mesh in the body and codend
Authors: Rotherham Douglas , Broadhurst Matt K. , Gray Charles A. , Johnson Daniel D. 
Published: April 2008

Abstract
Rotherham, D., Broadhurst, M. K., Gray, C. A., and Johnson, D. D. 2008. Developing a beam trawl for sampling estuarine fish and crustaceans: assessment of a codend cover and effects of different sizes of mesh in the body and codend. – ICES Journal of Marine Science, 65: 687–696. An experiment was carried out in the Clarence River (New South Wales, Australia) to test the hypotheses that fish and crustacean catches in an experimental beam trawl were affected by a codend cover and the sizes of mesh in the body and codend. The cover had no obvious effects on the catches retained in the codend. Similarly, in comparisons between trawl bodies made from 26- and 41-mm diamond-shaped mesh, there were no differences in the assemblages of fish caught, or in the mean numbers entering the codends. For one species of fish (Acanthopagrus australis), however, there were differences in the proportions caught between the trawl bodies across different size classes. There was also some evidence to suggest that mesh size in the body of the trawl influenced the size selection of school prawns (Metapenaeus macleayi). For most finfish, there were no differences in catches between codends made from 20-mm and from 29-mm mesh hung on the bar (i.e. square-shaped mesh). In contrast, mesh size in the codend was important for the size selectivity of school prawns, with smaller carapace lengths at 50% retention in the 20-mm codend. We conclude that use of a 41-mm mesh in the body and a 20-mm square mesh in the codend of the beam trawl would be appropriate for future sampling with this gear in estuaries of New South Wales. A similar experimental approach to ours is needed in adapting the beam trawl to estuaries in other parts of the world, or in developing other types of research trawl.
The evaluation of tailored and web‐based information for new fathers
Authors: Fletcher R. , Vimpani G. , Russell G. , Keatinge D. 
Published: April 2008

AbstractBackground  Information and advice on infant health and development have been shown to be well received by new parents and to lead to more confident and nurturing parenting. However, in spite of the accumulating evidence highlighting the importance of fathers to the well‐being of their families, fathers rarely access and utilize ‘parenting’ information. Tailored information for fathers delivered via email and Internet may provide an alternate route for support for fathers. This study aimed to assess father's readiness to utilize electronic information tailored to father's role.Methods  Two hundred and fifty‐three fathers from antenatal classes in two Australian cities were offered email and web‐based information on seven topics: baby play, breastfeeding, post‐natal depression, father–infant bonding, sex after birth, work–family balance and fussy babies. Of 137 who completed consent forms, a total of 105 fathers selected three topics and 67 fathers provided 149 topic evaluations.Results  Most respondents were from managerial, professional or skilled occupations and had higher educational qualifications than the general population of fathers. The most popular topics were those that related to father–infant interaction (baby games and father–infant bonding), and the least popular were breastfeeding and sex after the birth. Respondents rated the information as satisfactory and most (78%) indicated that it changed their approach to fathering. Although the websites provided were available through the Internet, few fathers had previously accessed them.Conclusions  Information tailored to new father's perspectives provided through email or Internet may increase new fathers' access to useful knowledge and support. Important health topics such as breastfeeding may not currently be perceived as particularly relevant to fathers in the antenatal period. Portals designed to filter existing websites could facilitate the use of parenting information by new fathers.
Updated growth curves for Turkish children aged 15 days to 60 months
Authors: Gökçay G. , Furman A. , Neyzi O. 
Published: April 2008

AbstractBackground  Growth reference values are useful in paediatric health care as a health indicator. Secular changes in height for age values are also known to affect the timing of puberty and brain weight. Different populations may be at different stages of this secular trend. It is, therefore, necessary to periodically update the growth reference values for each population to identify these changes. The aim of this study was to update the growth reference values for Turkish infants and young children.Methods  Background information and height/length, weight and head circumference measurements on a sample of 2391 boys and 2102 girls were obtained from Well Child Clinic Records. The LMS method was used for the analyses. The percentage of exclusive breastfeeding was 62% at 4 months and 26.6% at 6 months. The continuation rate of breastfeeding at 12 months was 62.5%.Results  Comparison with previous Turkish data showed an increase in height of 0.9 cm for boys and 1.1 cm for girls at age 5 years. The increase in weight was 0.220 kg in girls, while a decrease of 0.160 kg was noted in boys. Comparison with the 2000 US and Swedish values indicated that population differences may exist in pre‐pubertal years.Conclusion  This study provides an enhanced instrument to evaluate the growth of Turkish infants and young children.
Renal cell carcinoma marker reliably discriminates central nervous system haemangioblastoma from brain metastases of renal cell carcinoma
Authors: Ingold B , Wild P J , Nocito A , Amin M B , Storz M , Heppner F L , Moch H 
Published: April 2008

Aims:  The distinction between central nervous system (CNS) metastases of clear cell renal cell carcinoma (RCC) and CNS haemangioblastoma still poses a challenge to the pathologist. Since both entities occur in von Hippel–Lindau disease, this aggravates the issue. The antibody renal cell carcinoma marker (RCC‐ma) has been suggested to identify primary RCCs specifically, but its value for diagnosing metastases of RCC is controversial. The aim was to assess two distinct clones of the RCC‐ma for their potential to: (i) identify primary RCCs and (ii) differentiate between CNS metastases of clear cell RCC and CNS haemangioblastomas.Methods and results:  Using tissue microarrays, 77% (n = 363; PN‐15) and 66% (n = 355; 66.4C2) of clear cell RCCs, and 93% (PN‐15) and 74% (66.4C2) of papillary RCCs (n = 46) were immunopositive for RCC‐ma, whereas none of the investigated chromophobe RCCs (n = 22) or any of the oncocytomas (n = 15) showed immunoreactivity. Importantly, 50.9% of CNS metastases of clear cell RCCs (n = 55) exhibited RCC‐ma expression, whereas all CNS haemangioblastomas (71) were negative.Conclusions:  Both RCC‐ma clones, despite some variation in their sensitivity to detect clear cell and papillary RCCs, are of value in differentiating subtypes of primary RCC and are excellent markers for discriminating clear cell lesions in the brain.
Activated B cells modified by electroporation of multiple mRNAs encoding immune stimulatory molecules are comparable to mature dendritic cells in inducing in vitro antigen‐specific T‐cell responses
Authors: Lee Jaewoo , Dollins Claudia M. , Boczkowski David , Sullenger Bruce A. , Nair Smita 
Published: April 2008

Summary Ex‐vivo‐activated B cells are an alternative source of antigen‐presenting cells (APCs) and a potential replacement for dendritic cells (DCs) in immunotherapy. However, the ability of ex‐vivo‐activated B cells to function as potent APCs has been a concern, especially when compared to DCs. Our study investigated whether modification of activated B cells with immune stimulatory molecules could enhance the ability of activated B cells to stimulate T cells. We show that murine splenic B cells, activated with a combination of Toll‐like receptor agonist and agonistic anti‐CD40, stimulated antigen‐specific CD8+ T cells more efficiently than cells activated with Toll‐like receptor agonist or anti‐CD40 alone, probably by down‐regulation of the immune regulatory cytokine interleukin‐10 (IL‐10). However, the activated B cells were still poor T‐cell stimulators compared to mature DCs. Therefore, we modified the activated B cells by simultaneous electroporation of multiple messenger RNAs encoding costimulatory molecules (OX40L and 4‐1BBL), cytokines (IL‐12p35 and IL‐12p40) and antigen. We found that de novo expression or overexpression of OX40L, 4‐1BBL and IL‐12p70 on activated B cells synergistically enhanced proliferation as well as IL‐2 and interferon‐γ production by CD8+ T cells. Furthermore, the RNA‐modified activated B cells induced antigen‐specific cytotoxic T lymphocyte responses as efficiently as mature DCs in vitro. Unexpectedly, modified activated B cells were inferior to mature DCs at in vivo induction of CD8+ T‐cell responses. In summary, activated B cells modified to express immune stimulatory molecules are a potent alternative to DCs in immunotherapy.
How ethical is ethical research? Recruiting marginalized, vulnerable groups into health services research
Authors: Smith Linda J. 
Published: April 2008

AbstractTitle.  How ethical is ethical research? Recruiting marginalized, vulnerable groups into health services research. Aim.  This paper is a discussion of how tensions in research ethics guidelines can have an impact on the recruitment of marginalized, vulnerable groups of people into health services research.Background.  Research ethics guidelines in the United Kingdom (UK) predominantly reflect requirements for clinical trials and medical research but apply to all types of research conducted in the National Health Service. Guidelines emphasize the process of informed consent to protect individuals’ autonomy and rights, and avoid harm to vulnerable people. This focus, however, can result in the exclusion of and discrimination against marginalized groups at a time when user involvement in research and health service developments is increasingly emphasized in policy.Method.  This paper is based on a critical reflection on tensions observed in current research ethics guidelines in the UK. These tensions became apparent following recruitment of nine postnatal drug‐using women to a qualitative phase of an evaluation in 2005 of a specialist health visitor service.Findings.  The main ethical tensions identified concerned the sampling and recruitment of marginalized groups, which can affect the validity and reliability of research findings. Consideration needs to be given to sampling and accessing such groups and assessing the capacity of individuals to give informed consent. This is to avoid coercion and exploitation of vulnerable individuals and groups in research, increase validity and reliability, and avoid pre‐emptive exclusion of such groups in the research design.Conclusion.  Ethical judgements and decisions about research can be contradictory and be influenced by competing paradigms. Use of the concept of ‘responsible advocacy’, with due consideration to the principles of autonomy, beneficence, non‐maleficence and justice, is recommended.
Nurses’ perceptions of evidence‐based nursing practice
Authors: Koehn Mary L. , Lehman Karen 
Published: April 2008

AbstractTitle.  Nurses’ perceptions of evidence‐based nursing practice. Aim.  This paper is a report of a study to investigate Registered Nurses’ perceptions, attitudes and knowledge/skills associated with evidence‐based practice.Background.  Evidence‐based practice has emerged as a marker for healthcare quality. Previous studies have primarily used researcher‐developed descriptive surveys to examine nurses’ perceptions, as well as facilitators and barriers, related to evidence‐based practice. Research suggests the value of understanding the organizational context prior to taking steps to implement evidence‐based practice.Methods.  This study, conducted in 2006, had a descriptive, cross‐sectional survey design using a psychometrically‐validated measure of evidence‐based practice. All Registered Nurses (n = 1031) employed by a large medical centre in the United States of America were asked to complete the questionnaires. The final response rate was 40·9% (n = 422).Findings.  Participants had moderate scores on practice and attitudes towards evidence‐based practice. The knowledge/skills mean scores were somewhat lower. Statistically significant differences were found for attitudes between those with baccalaureate and higher education compared to those with associate and diploma education. The two most cited barriers to implementing evidence‐based practice were time and knowledge.Conclusion.  The findings suggest the value of a methodical assessment when developing a systematic plan for implementing an institutional culture of evidence‐based practice.
Kinematics of massive stars in the Small Magellanic Cloud
Authors: Evans Christopher J. , Howarth Ian D. 
Published: April 2008

Abstract
We present radial velocities for 2045 stars in the Small Magellanic Cloud (SMC), obtained from the 2dF survey by Evans et al. The great majority of these stars are of OBA type, tracing the dynamics of the young stellar population. Dividing the sample into ad hoc ‘bar’ and ‘wing’ samples (north and south, respectively, of the line: δ=−77°50′+[4α]′, where α is the right ascension in minutes of time) we find that the velocities in the SMC bar show a gradient of 26.3 ± 1.6 km s−1 deg−1 at a position angle of 126°± 4°. The derived gradient in the bar is robust to the adopted line of demarcation between the two samples. The largest redshifts are found in the SMC wing, in which the velocity distribution appears distinct from that in the bar, most probably a consequence of the interaction between the Magellanic Clouds that is predicted to have occurred 0.2 Gyr ago. The mean velocity for all stars in the sample is +172.0 ± 0.2 km s−1 (redshifted by ∼20 km s−1 when compared to published results for older populations), with a velocity dispersion of 30 km s−1.
Airway inflammation in obese and nonobese patients with difficult‐to‐treat asthma
Authors: Van Veen I. H. , Ten Brinke A. , Sterk P. J. , Rabe K. F. , Bel E. H. 
Published: April 2008

Background:  Asthma and obesity are associated disorders, but the contribution of obesity to difficult‐to‐treat asthma as well as the mechanisms responsible for this relationship are unclear. The aim of this study was to investigate the relationship between obesity (body mass index ≥ 30) and factors related with asthma severity in patients with difficult‐to‐treat asthma.Methods:  One hundred and thirty‐six nonsmoking asthmatic adults with persistent symptoms despite high doses of inhaled or oral corticosteroids and long‐acting bronchodilators were studied [70% female, median (range) age 44.6 (18–75) years, 32% on daily oral corticosteroids]. The association between obesity, lung function parameters [forced expiratory volume in 1 s (FEV1), functional residual capacity/total lung capacity (FRC/TLC)], inflammatory markers [blood eosinophils, sputum eosinophils and neutrophils, exhaled nitric oxide (FENO), airway hyperresponsiveness, C‐reactive protein (CRP)] and aggravating co‐morbid factors (severe chronic sinus disease, gastro‐esophageal reflux, recurrent respiratory infections, psychopathology and obstructive sleep apnea) was investigated.Results:  Obese patients (n = 29) had a higher FEV1%pred (P = 0.05) and a lower FRC/TLC%pred (P < 0.01) compared with nonobese patients (n = 107). Body mass index was inversely related with sputum eosinophils (r = −0.36, P < 0.01) and FENO (r = −0.30, P < 0.01). Obese patients had an increased risk for gastro‐esophageal reflux (OR = 2.3) and sleep apnea (OR = 3.1).Conclusion:  Obesity in patients with difficult‐to‐treat asthma is inversely related with sputum eosinophils and FENO, and positively associated with the presence of co‐morbid factors and reduced lung volumes. This suggests that other factors than airway inflammation alone explain the relationship between obesity and asthma severity.
Carbohydrate‐based particles reduce allergic inflammation in a mouse model for cat allergy
Authors: Neimert‐Andersson T. , Thunberg S. , Swedin L. , Wiedermann U. , Jacobsson‐Ekman G. , Dahlén S.‐E. , Scheynius A. , Grönlund H. , Hage M. van , Gafvelin G. 
Published: April 2008

Background:  Allergen‐specific immunotherapy (ASIT) is the only treatment of allergic disease that gives long‐lasting relief of symptoms. However, concerns for safety and efficiency have highlighted the need for improvement of the therapy. We have previously suggested carbohydrate‐based particles (CBPs) as a novel adjuvant and allergen carrier for ASIT. Our aim of this study was to evaluate the therapeutic potential of CBPs in ASIT, employing a mouse model for cat allergy.Methods:  BALB/c mice were subcutaneously immunized with the recombinant (r) cat allergen Fel d 1 followed by intranasal challenge with cat dander extract (CDE). The sensitized mice were therapeutically treated with rFel d 1 covalently coupled to CBPs (CBP‐rFel d 1). Airway hyper‐reactivity (AHR), infiltration of leucocytes in bronchoalveolar lavage (BAL) fluid, allergen‐specific serum immunoglobulin levels and in vitro splenocyte responses were evaluated.Results:  Mice treated with CBP‐rFel d 1 showed reduced features of allergic inflammation. They responded with (i) significantly decreased AHR and infiltration of eosinophils in BAL fluid after CDE challenge, (ii) the serum level of rFel d 1‐specific IgE was reduced and the level of IgG2a was more pronounced after CBP‐rFel d 1 treatment, and (iii) there was also a tendency of decreased allergen‐specific cellular response.Conclusions:  Carbohydrate‐based particles are effective tools as adjuvant and allergen carriers for use in ASIT and constitutes a promising strategy to improve allergy treatment.