bluuebunny/crossref_metadata_2025_split huggingface dataset:
Evaluation of Compliance with the EGS Guidelines in Spain, Using Achievable Benchmarks of Care (ABC®) methodology: The IMCA Study
Authors: Castejón-Cervero Miguel A. , Jiménez-Parras Rafael , Fernandez-Arias Isabel , Teus-Guezala Miguel A. ,   IMCA Study Group
Published: November 2010

Purpose TO evaluate compliance with diagnostic and therapeutic recommendations of the European Glaucoma Society (EGS) for the management of glaucoma in Spain, as determined using the Achievable Benchmarks of Care approach. Methods A panel of 3 experts extracted quality and process-of-care indicators from the EGS guidelines. Investigators from all over the country, representative of Spanish ophthalmologists, were invited to participate in the study, completing a questionnaire on quality indicators (pertaining to the center) and process-of-care indicators (pertaining to all patients) for the first, diagnostic visit (retrospective) and the study visit. Results A total of 495 Spanish ophthalmologists included 5,060 patients with glaucoma or intraocular hypertension. The treatment was initiated with monotherapy in 88.5% of the patients. Overall, the percentage compliance with diagnostic examinations was 84.6% for intraocular pressure measurement, 96.3% for optic nerve head evaluation, 76.6% for visual field evaluation, 29.5% for central corneal thickness evaluation, and 49.3% at the study visit. The benchmark performance was close to 100% for most examinations. Only 32.8% of the centres had a written protocol for the management of the patients with glaucoma, and in these centers the recommendations of the EGS were followed in a higher proportion (p<0.0001) than in the rest. Conclusions The use of local protocols for the management of glaucoma seems to enhance compliance. Benchmark performance was close to 100% in most indicators, suggesting that EGS recommendations are attainable in Spain. The overall performance suggests that certain diagnostic procedures are, in practice, not as widely used as recommended.
Statistical confidence measures for genome maps: application to the validation of genome assemblies
Authors: Servin Bertrand , de Givry Simon , Faraut Thomas 
Published: November 2010

Abstract
Motivation: Genome maps are imperative to address the genetic basis of the biology of an organism. While a growing number of genomes are being sequenced providing the ultimate genome maps—this being done at an even faster pace now using new generation sequencers—the process of constructing intermediate maps to build and validate a genome assembly remains an important component for producing complete genome sequences. However, current mapping approach lack statistical confidence measures necessary to identify precisely relevant inconsistencies between a genome map and an assembly.
Results: We propose new methods to derive statistical measures of confidence on genome maps using a comparative model for radiation hybrid data. We describe algorithms allowing to (i) sample from a distribution of maps and (ii) exploit this distribution to construct robust maps. We provide an example of application of these methods on a dog dataset that demonstrates the interest of our approach.
Availability: Methods are implemented in two freely available softwares: Carthagene (http://www.inra.fr/mia/T/CarthaGene/) and a companion software (metamap, available at: http://snp.toulouse.inra.fr/~servin/index.cgi/Metamap)
Contact: Bertrand.Servin@toulouse.inra.fr
Supplementary information: Supplementary data are available at Bioinformatics online.
Automated construction and testing of multi-locus gene–gene associations
Authors: Abo Ryan , Knight Stacey , Thomas Alun , Camp Nicola J. 
Published: November 2010

AbstractSummary: It has been argued that the missing heritability in common diseases may be in part due to rare variants and gene–gene effects. Haplotype analyses provide more power for rare variants and joint analyses across genes can address multi-gene effects. Currently, methods are lacking to perform joint multi-locus association analyses across more than one gene/region. Here, we present a haplotype-mining gene–gene analysis method, which considers multi-locus data for two genes/regions simultaneously. This approach extends our single region haplotype-mining algorithm, hapConstructor, to two genes/regions. It allows construction of multi-locus SNP sets at both genes and tests joint gene–gene effects and interactions between single variants or haplotype combinations. A Monte Carlo framework is used to provide statistical significance assessment of the joint and interaction statistics, thus the method can also be used with related individuals. This tool provides a flexible data-mining approach to identifying gene–gene effects that otherwise is currently unavailable.Availability: http://bioinformatics.med.utah.edu/Genie/hapConstructor.htmlContact: ryan.abo@hsc.utah.edu
PLEXY: efficient target prediction for box C/D snoRNAs
Authors: Kehr Stephanie , Bartschat Sebastian , Stadler Peter F. , Tafer Hakim 
Published: November 2010

Abstract
Motivation: Small nucleolar RNAs (snoRNAs) are an abundant class of non-coding RNAs with a wide variety of cellular functions including chemical modification of RNA, telomere maintanance, pre-rRNA processing and regulatory activities in alternative splicing. The main role of box C/D snoRNAs is to determine the targets for 2′-O-ribose methylation, which is important for rRNA maturation and splicing regulation of some mRNAs. The targets are still unknown, however, for many ‘orphan’ snoRNAs. While a fast and efficient target predictor for box H/ACA snoRNAs is available, no comparable tool exists for box C/D snoRNAs, even though they bind to their targets in a much less complex manner.
Results: PLEXY is a dynamic programming algorithm that computes thermodynamically optimal interactions of a box C/D snoRNA with a putative target RNA. Implemented as scanner for large input sequences and equipped with filters on the duplex structure, PLEXY is an efficient and reliable tool for the prediction of box C/D snoRNA target sites.
Availability: The perl script PLEXY is freely available at http://www.bioinf.uni-leipzig.de/Software/PLEXY.
Contact: steffi@bioinf.uni-leipzig.de
Supplementary Information: Supplementary data are available at Bioinformatics online.
Antiarrhythmics After Ablation of Atrial Fibrillation (5A Study)
Authors: Leong-Sit Peter , Roux Jean-Francois , Zado Erica , Callans David J. , Garcia Fermin , Lin David , Marchlinski Francis E. , Bala Rupa , Dixit Sanjay , Riley Michael , Hutchinson Mathew D. , Cooper Joshua , Russo Andrea M. , Verdino Ralph , Gerstenfeld Edward P. 
Published: November 2010

Background—
We previously demonstrated that treatment with antiarrhythmic drugs (AADs) during the first 6 weeks after atrial fibrillation (AF) ablation reduces the incidence of clinically significant atrial arrhythmias and need for cardioversion or hospitalization for arrhythmia management. Whether early rhythm suppression decreases longer-term arrhythmia recurrence is unknown. We now report the 6-month follow-up data from this study.

Methods and Results—

The Antiarrhythmics After Ablation of Atrial Fibrillation study prospectively randomized patients with paroxysmal AF undergoing ablation to either receive (AAD group) or not receive (no-AAD group) AAD treatment for the first 6 weeks after ablation; all patients received atrioventricular nodal blockers. Physicians were encouraged to stop the AADs after the 6-week treatment period. All patients underwent 4 weeks of transtelephonic monitoring to document asymptomatic AF and an evaluation at 6 weeks and 6 months. A total of 110 patients (71% men) aged 55±9 years were randomized, with 53 to AAD and 57 to no AAD. At 6 months, there was no difference in freedom from AF between the early AAD and no-AAD groups (38/53 [72%] versus 39/57 [68%];
P
=0.84). Lack of early AF recurrence during the initial 6-week period was the only independent predictor of 6-month freedom from AF (64/76 [84%] without early recurrence versus 13/34 [38%] with early recurrence;
P
=0.0001).

Conclusions—
Although short-term use of AADs after AF ablation decreases early recurrence of atrial arrhythmias, early use of AADs does not prevent arrhythmia recurrence at 6 months. Early AF recurrence on or off AADs during the initial 6-week blanking period is a strong independent predictor of long-term AF recurrence.

Clinical Trial Registration—

URL:
http://www.clinicaltrials.gov
. Unique identifier: NCT00408200.
Incidence, Determinants, and Prognostic Implications of True Pleomorphism of Ventricular Tachycardia in Patients With Implantable Cardioverter-Defribillators
Authors: Hadid Claudio , Almendral Jesus , Ortiz Mercedes , Schwab Joerg Otto , Janko Sabine , Mischke Karl , Arribas Fernando , Wolpert Christian , Ricci Renato , Adragao Pedro , Cobo Erik , Navarro Xavier , Quesada Aurelio 
Published: November 2010

Background—
The occurrence of monomorphic ventricular tachycardia (M-VT) with >1 QRS morphology during the same episode (pleomorphism [PL]) or in different episodes (multiple morphologies [MM]) has been described through ECG. Implantable cardioverter-defribillator (ICD) electrograms (EGs) provide the opportunity to analyze virtually all spontaneous M-VT episodes. We sought to study the incidence, determinants, and prognostic significance of PL and MM as assessed by ICD-EG in a prospective series of patients with ICDs.

Methods and Results—

Spontaneous episodes of M-VT were analyzed before ICD intervention. PL was defined as >1 ICD-EG morphology, each having ≥6 consecutive identical beats during the same VT episode, and MM as >1 ICD-EG morphology in different M-VT episodes in the same patient. We analyzed 1881 M-VT episodes from 315 patients followed for 17 months. PL and MM occurred in 6% and 19%, respectively, of the total population (16% and 62% of patients with M-VT). Recurrent M-VT as diagnosis for ICD indication predicted PL and MM. Patients with PL more frequently developed MM (85% versus 15%;
P
<0.001) compared to patients without PL. Total mortality (5%) was significantly higher in patients with PL (20%), in patients with MM (11.5%), and in women (12%). In multivariate analysis, only PL (odds ratio, 5.33;
P
=0.009) and female sex (odds ratio, 3.1;
P
=0.038) predicted mortality.

Conclusions—
In a prospective series of patients with ICDs, mostly indicated for secondary prevention, both PL and MM of VT, as judged by ICD-EG, were not uncommon and were strongly associated. Female sex and the development of PL VT were the only independent predictors of mortality.
Association of Chronic Kidney Disease With Atrial Fibrillation Among Adults in the United States
Authors: Baber Usman , Howard Virginia J. , Halperin Jonathan L. , Soliman Elsayed Z. , Zhang Xiao , McClellan William , Warnock David G. , Muntner Paul 
Published: November 2010

Background—
Atrial fibrillation (AF) is common among patients with end-stage renal disease, but few data are available on its prevalence among adults with chronic kidney disease (CKD) of lesser severity.

Methods and Results—

We evaluated the association of CKD with ECG-detected AF among 26 917 participants in the REasons for Geographic and Racial Differences in Stroke (REGARDS) study, a population-based cohort of African-American and white US adults ≥45 years of age. Estimated glomerular filtration rate (eGFR) was calculated using the abbreviated Modification of Diet in Renal Disease study equation and albuminuria was defined as a urinary albumin to creatinine ratio ≥30 mg/g. Participants were categorized by renal function: no CKD (eGFR ≥60 mL/min/1.73 m
2
without albuminuria, n=21 081), stage 1 to 2 CKD (eGFR ≥60 mL/min/1.73 m
2
with albuminuria n=2938), stage 3 CKD (eGFR 30 to 59 mL/min/1.73 m
2
, n=2683) and stage 4 to 5 CKD (eGFR <30 mL/min/1.73 m
2
, n=215). The prevalence of AF among participants without CKD, and with stage 1 to 2, stage 3, and stage 4 to 5 CKD was 1.0%, 2.8%, 2.7% and 4.2%, respectively. Compared with participants without CKD, the age-, race-, and sex-adjusted odds ratios for prevalent AF were 2.67 (95% confidence interval, 2.04 to 3.48), 1.68 (95% confidence interval, 1.26 to 2.24) and 3.52 (95% confidence interval, 1.73 to 7.15) among those with stage 1 to 2, stage 3, and stage 4 to 5 CKD. The association between CKD and prevalent AF remained statistically significant after further multivariable adjustment and was consistent across numerous subgroups.

Conclusions—
Regardless of severity, CKD is associated with an increased prevalence of AF among US adults.
The passive transfer of immunoglobulin G serum antibodies from patients with longstanding Complex Regional Pain Syndrome
Authors: Goebell Andreas , Leitel Maria I. , Yangl Li , Deaconl Robert , Cendanl Cruz M. , Fox‐Lewisl Andrew , Vincentl Angela 
Published: November 2010

AbstractBackground: The aetiology of Complex Regional Pain Syndrome (CRPS) is unknown. Recent evidence suggests that there may be autoantibodies directed against peripheral nerves, but it is unclear whether such autoantibodies are merely biomarkers or whether they cause or contribute to the underlying pathology. The transfer of disease after injection of a patient's serum or IgG fraction into mice (‘passive transfer’) is the classic way to demonstrate a functional role of autoantibodies.Aims: Based on previous preliminary results, we wished to investigate whether the transfer of IgG antibodies affected mouse behaviour or produced signs of CRPS.Methods: We injected purified serum‐IgG from 12 patients and 12 controls into groups of 6–10 mice (∼17 mg/mouse intraperitoneally) on 2 consecutive days and looked for any evidence for altered behaviour or signs of CRPS. The observer, blinded as to test or control group, measured behaviour in the open field, stimulus‐evoked pain and motor coordination, and inspected limbs for autonomic CRPS signs.Results: Stimulus‐evoked pain and autonomic signs were not detected, but CRPS‐IgG induced significant depression of rearing behaviour (17.9 rears/3 min (n =84) vs. 22.1 rears/3 min (n =83), p =0.0004), confirming previous observations in a single case study. Moreover, motor impairment, one of the four cardinal signs of CRPS, was evident in the three CRPS‐IgG injected groups tested with a sensitive rota‐rod protocol (p <0.0001 vs. control‐IgG injected groups).Conclusions: These results lend support to a pathophysiological role for IgG autoantibodies in CRPS.
Metabolomic changes in autopsy‐confirmed Alzheimer's disease
Authors: Kaddurah‐Daouk Rima , Rozen Steve , Matson Wayne , Han Xianlin , Hulette Christine M. , Burke James R. , Doraiswamy P. Murali , Welsh‐Bohmer Kathleen A. 
Published: November 2010

BackgroundMetabolomics, the global science of biochemistry, provides powerful tools to map perturbations in the metabolic network and enables simultaneous quantification of several metabolites to identify metabolic perturbances that might provide insights into disease.MethodsIn this pilot study, we took a targeted electrochemistry‐based metabolomics approach where liquid chromatography followed by coulometric array detection enables quantification of over 30 metabolites within key neurotransmitter pathways (dopamine and serotonin) and pathways involved in oxidative stress.ResultsUsing samples from postmortem ventricular cerebrospinal fluid (15 Alzheimer's disease [AD] and 15 nondemented subjects with autopsy‐confirmed diagnoses) and by using regression models, correlations, Wilcoxon rank‐sum tests, and t‐tests we identified alterations in tyrosine, tryptophan, purine, and tocopherol pathways in patients with AD. Reductions in norepinephrine and its related metabolites were also seen, consistent with previously published data.ConclusionsThese data support further investigation of metabolomics in larger samples of clinical AD as well as in those with preclinical disease for use as biomarkers.
Differential effects of chromatin regulators and transcription factors on gene regulation: a nucleosomal perspective
Authors: Dong Dong , Shao Xiaojian , Zhang Zhaolei 
Published: November 2010

Abstract
Motivation: Chromatin regulators (CR) and transcription factors (TF) are important trans-acting factors regulating transcription process, and many efforts have been devoted to understand their underlying mechanisms in gene regulation. However, the influences of CR and TF regulation effects on nucleosomes during transcription are still minimally understood, and it remains to be determined the extent to which CR and TF regulatory effect shape the organization of nucleosomes in the genome. In this article we attempted to address this problem and examine the patterns of CR and TF regulation effects from the nucleosome perspective.
Results: Our results show that the CR and TF regulatory effects exhibit different paradigms of transcriptional control in Saccharomyces cerevisiae. We grouped yeast genes into two categories, ‘CR-sensitive’ genes and ‘TF-sensitive’ genes, based on how their expression profiles change upon deletion of CRs or TFs. We found that genes in these two groups have very different patterns of nucleosome organization. The promoters of CR-sensitive genes tend to have higher nucleosome occupancy, whereas the promoters of TF-sensitive genes are depleted of nucleosomes. Furthermore, the nucleosome profiles of CR-sensitive genes tend to show more dynamic characteristics than TF-sensitive genes. These results reveal that the nucleosome organizations of yeast genes have a strong impact on their mode of regulation, and there are differential regulation effects on nucleosomes between CRs and TFs.
Availability: http://www.utoronto.ca/zhanglab/papers/bioinfo_2010/
Contact: zhaolei.zhang@utoronto.ca
Supplementary information: Supplementary data are available at Bioinformatics online.
Electrochemical hydrogenation and corrosion studies of Ti‐48Al‐2Cr‐2Nb alloy in acidic solution
Authors: Arockiasamy Antonyraj , Eliezer Dan , Wang Paul T. , Horstemeyer M.F. , King Roger L. 
Published: November 2010

PurposeThe aim of this paper is to investigate the effect of cathodic charging and corrosion behavior of Ti‐48Al‐2Cr‐2Nb alloy in hydrochloric acid solutions.Design/methodology/approachTiAl alloy specimens of thickness 0.5 mm were cathodically charged in 0.1 M HCl solution at room temperature. The prominent current densities selected for this investigation were 25 and 50 mA cm−2 for durations of 24‐120 h. The change in weight of the specimen after charging was measured by a microbalance with an accuracy of ±1 μg.FindingsThe nature of the specimen surfaces was characterized by X‐ray diffraction (XRD), auger electron spectroscopy (AES) and scanning electron microscopy (SEM) equipped with energy dispersive X‐ray spectroscopy (EDS). XRD revealed the phase transformation from microcrystalline to nano‐crystalline, particularly after high charging times (120 h) and high current density (50 mA cm−2). AES and EDS further assessed the compositional fluctuations on both cathodically charged and potentiodynamically polarized specimens. Surface corrosion leading to the generation of microcracks throughout the surface region was observed by SEM. Cathodic charging and the polarization process were responsible for embrittlement and pitting. Decreases in both weight and Vickers hardness values with an increase in charging time revealed that surface erosion depended strongly upon charging density.Originality/valueThe results presented in this work shed light on the role of alloying elements the passive behavior and their implications on their stability in hydrochloric acid environments.
Breaking the barriers: the role of support companies in making open source a reality
Authors: Dimant Nick 
Published: November 2010

PurposeThe purpose of this paper is to look at how the library sector might benefit from open source, from the point of view of the current vendor/owner of Koha, an open source library management system.Design/methodology/approachThe paper is based on the author's experience in the library systems market.FindingsThe paper finds that increasing numbers of libraries are migrating from the major proprietary vendors to both Evergreen and Koha.Originality/valueThe vendor viewpoint supplies the value of this paper.
Developing Tanzanian civil society
Authors: Banjac Marinko 
Published: November 2010

PurposeThe development of Tanzanian civil society is widely understood to be one of the key processes in the democratization of the country, and this vision is also shared by the World Bank. The purpose of this paper is to analyze the intention and impact of World Bank policies aimed at supporting Tanzanian civil society organizations.Design/methodology/approachThe paper uses the Lacanian psychoanalytic approach combined with Foucault's notion of governmentality as a conceptual tool. Within this theoretical framework, a specific World Bank programme in Tanzania, the Social Development Civil Society Fund, is analyzed.FindingsDeveloped democratic states produce, through the World Bank, the desires of not‐yet‐fully democratic countries to embrace the benefits that (democratic) development can bring. The World Bank programme aimed at the development of Tanzanian civil society is formulated in a way that posits Tanzania as a not‐yet‐fully democratic country. This is achieved through the World Bank's advice and recommendations, which trigger the desires of Tanzanians to participate in development and thus to achieve (always elusive) prosperity and democracy. Moreover, the World Bank programme can be seen as an ensemble of governmental practices advancing the idea of self‐empowerment through which Tanzanians are made governable.Originality/valueThe paper contributes to the understanding of democratic transition, from the perspective of Lacanian psychoanalysis, as a social fantasy that plays a crucial role in the constitution of global hierarchical relationships and in the construction of the identities of so‐called democratic states and not‐yet‐fully democratic countries. Within this scheme, the World Bank's policies are governmental technologies that trigger desires of not‐yet‐fully democratic countries.
On identity reformation and local transition: a case from Poland
Authors: Joanna Bourne Dorota 
Published: November 2010

PurposeThe purpose of this paper is to explore and understand the process of successful introduction of total quality management (TQM) in Poland and the way in which it impacted on identity of Polish managers.Design/methodology/approachThe study is based on a combination of ethnographic research and repertory grid interviews.FindingsThe process of TQM introduction and implementation is examined through the application of translation as a model incorporating cultural and socio‐economical dimensions in addition to individual and organizational levels that shaped the development of TQM in Poland. It then draws on the idea of fantasy as theorized in Lacanian psychoanalysis in order to incorporate the unconscious element of translation process which is missing from Latour's theorization and which forms an important aspect of adoption of new technology and the emergence of a new post‐transition generation of managers in Poland. The paper argues that a complex combination of contextual factors, amongst them the notion of fantasy shaped the process of translation of TQM to Poland, the identity formation of Polish managers and to the emergence of a new post‐transition generation of managers in Poland.Originality/valueThis paper contributes to the literature on the post‐command transition by illustrating this process through the fantasy of total quality management explored in a specific socio‐cultural and geographical context and by combining the idea of Latour's translation with Lacanian fantasy.