bluuebunny/crossref_metadata_2025_split huggingface dataset:
Interests versus culture in the theory of institutional change?
Authors: ZWEYNERT JOACHIM 
Published: October 2009

Abstract:In Douglass C. North's works on institutional change, his focus shifted from formal institutions and highly rational actors to the links between culture, cognition, and the evolution of institutions. This has led to a corresponding shift in his basic explanation of institutional change: In his earlier works, institutional change is mainly caused by actions of highly rational utility-maximizing political actors. In his later works, the evolution of a society's institutions is above all a function of changes in the dominant belief system. The paper tries to contribute to the obvious task of bringing these two explanations of institutional change together. My synthetic approach rests basically on a Northian framework supplemented with three further elements: firstly, with the idea of the transfer of institutions; secondly, with the concept of functional differentiation; and, thirdly, and decisively, with an understanding of culture as a toolkit, leaving room for interest, choice, and strategic action.
Risk Factors for Mortality in Patients with NosocomialStenotrophomonas maltophiliaPneumonia
Authors: Tseng Chia-Cheng , Fang Wen-Feng , Huang Kuo-Tung , Chang Pei-Wen , Tu Mei-Lien , Shiang Yi-Ping , Douglas I. S. , Lin Meng-Chih 
Published: October 2009

Objective.The aim of this study was to determine potential risk factors for mortality in patients with nosocomialStenotrophomonas maltophiliapneumonia.Design.A retrospective, single-center, observational study.Setting.A 2400-bed tertiary teaching hospital in southern Taiwan.Patients and Methods.This retrospective study evaluated patients (age, at least 18 years) with nosocomial pneumonia (S. maltophiliaisolated from respiratory culture) who were seen at Kaohsiung Chang Gung Memorial Hospital over a 3-year period. A total of 406 patients (64% male, mean age ± standard deviation, 69.6 ± 14.93 years; mean duration of hospital stay ± standard deviation, 57.5 ± 39.47 days) were included.Results.Most index isolates (53.9%) were from the first sample cultured. Polymicrobial isolates were cultured from samples from 177 (43.6%) of the 406 study patients. The most common copathogen wasPseudomonas aeruginosa(53.11% of isolates). The all-cause hospital mortality rate was 42.6% (173 deaths among 406 patients). Survivors had a shorter time from admission to a positive index culture result than did nonsurvivors (26.1 vs 31.7 days;P= .04). Mortality was significantly higher among patients with malignancy (adjusted odds ratio [AOR], 2.48; 95% confidence interval [CI], 1.52–4.07;P< .001 ), renal disease (AOR, 2.6; 95% CI, 1.51–4.47;P= .001), intensive care unit stay (AOR, 1.72; 95% CI, 1.1–2.7;P= .018), and inadequate initial empirical antibiotic therapy (AOR, 2.17; 95% CI, 1.4–3.38;P= .001).Conclusions.S. maltophiliapneumonia is associated with a high mortality rate and is commonly associated with concomitant polymicrobial colonization or infection. Underlying comorbidities and inadequate initial empirical antibiotic therapy substantially account for increased mortality rates.
Ancestors 1.0: a web server for ancestral sequence reconstruction
Authors: Diallo Abdoulaye Banire , Makarenkov Vladimir , Blanchette Mathieu 
Published: October 2009

Abstract
Summary: The computational inference of ancestral genomes consists of five difficult steps: identifying syntenic regions, inferring ancestral arrangement of syntenic regions, aligning multiple sequences, reconstructing the insertion and deletion history and finally inferring substitutions. Each of these steps have received lot of attention in the past years. However, there currently exists no framework that integrates all of the different steps in an easy workflow. Here, we introduce Ancestors 1.0, a web server allowing one to easily and quickly perform the last three steps of the ancestral genome reconstruction procedure. It implements several alignment algorithms, an indel maximum likelihood solver and a context-dependent maximum likelihood substitution inference algorithm. The results presented by the server include the posterior probabilities for the last two steps of the ancestral genome reconstruction and the expected error rate of each ancestral base prediction.
Availability: The Ancestors 1.0 is available at http://ancestors.bioinfo.uqam.ca/ancestorWeb/.
Contact: diallo.abdoulaye@uqam.ca
Evaluation of linguistic features useful in extraction of interactions from PubMed; Application to annotating known, high-throughput and predicted interactions in I2D
Authors: Niu Yun , Otasek David , Jurisica Igor 
Published: October 2009

Abstract
Motivation: Identification and characterization of protein–protein interactions (PPIs) is one of the key aims in biological research. While previous research in text mining has made substantial progress in automatic PPI detection from literature, the need to improve the precision and recall of the process remains. More accurate PPI detection will also improve the ability to extract experimental data related to PPIs and provide multiple evidence for each interaction.
Results: We developed an interaction detection method and explored the usefulness of various features in automatically identifying PPIs in text. The results show that our approach outperforms other systems using the AImed dataset. In the tests where our system achieves better precision with reduced recall, we discuss possible approaches for improvement. In addition to test datasets, we evaluated the performance on interactions from five human-curated databases—BIND, DIP, HPRD, IntAct and MINT—where our system consistently identified evidence for ∼60% of interactions when both proteins appear in at least one sentence in the PubMed abstract. We then applied the system to extract articles from PubMed to annotate known, high-throughput and interologous interactions in I2D.
Availability: The data and software are available at: http://www.cs.utoronto.ca/∼juris/data/BI09/.
Contact: yniu@uhnres.utoronto.ca; juris@ai.utoronto.ca
Supplementary information: Supplementary data are available at Bioinformatics online.
Identification of non-Hodgkin's lymphoma prognosis signatures using the CTGDR method
Authors: Ma Shuangge , Zhang Yawei , Huang Jian , Han Xuesong , Holford Theodore , Lan Qing , Rothman Nathaniel , Boyle Peter , Zheng Tongzhang 
Published: October 2009

Abstract
Motivation: Although NHL (non-Hodgkin's lymphoma) is the fifth leading cause of cancer incidence and mortality in the USA, it remains poorly understood and is largely incurable. Biomedical studies have shown that genomic variations, measured with SNPs (single nucleotide polymorphisms) in genes, may have independent predictive power for disease-free survival in NHL patients beyond clinical measurements.
Results: We apply the CTGDR (clustering threshold gradient directed regularization) method to genetic association studies using SNPs, analyze data from an association study of NHL and identify prognosis signatures to diffuse large B cell lymphoma (DLBCL) and follicular lymphoma (FL), the two most common subtypes of NHL. With the CTGDR method, we are able to account for the joint effects of multiple genes/SNPs, whereas most existing studies are single-marker based. In addition, we are able to account for the ‘gene and SNP-within-gene’ hierarchical structure and identify not only predictive genes but also predictive SNPs within identified genes. In contrast, existing studies are limited to either gene or SNP identification, but not both. We propose using resampling methods to evaluate the predictive power and reproducibility of identified genes and SNPs. Simulation study and data analysis suggest satisfactory performance of the CTGDR method.
Contact: shuangge.ma@yale.edu
Supplementary information: Supplementary data are available at Bioinformatics online.
Phylogeny, biogeography and the stepwise evolutionary colonization of intertidal habitat in the Liparocephalini based on morphological and molecular characters (Coleoptera: Staphylinidae: Aleocharinae)
Authors: Ahn Kee‐Jeong , Jeon Mi‐Jeong , Branham Marc A. 
Published: October 2009

AbstractA phylogenetic analysis of the tribe Liparocephalini Fenyes is presented based on morphological and molecular characters. The data set comprised 50 adult morphological characters, partial COI (907 bp), COII (366 bp) and 12S rDNA (325–355 bp), and nearly complete sequences of 18S rDNA (1768–1902 bp) for 21 species. Eighteen species of liparocephaline beetles from all eight genera and three outgroups, are included. The sequences were analysed separately and simultaneously with morphological characters by direct optimization in the program POY4 and by partitioned Bayesian analysis for the combined data. The direct optimization (DO) tree for the combined data under equal weighting, which also shows a minimum incongruence length difference value, resulted in a monophyletic Liparocephalini with the following patterns of phylogenetic relationships (outgroup ((Baeostethus,Ianmoorea) (Paramblopusa((Amblopusa,Halorhadinus) (Liparocephalus,Diaulota))))). A sensitivity analysis using 16 different parameter sets for the combined data shows the monophyly of the liparocephalines and all its genera under all parameter sets. Bayesian analysis resulted in topological differences in comparison with the DO tree under equal weighting only in the position of the genusParamblopusaand clade (Amblopusa + Halorhadinus), which were reversed. Historical biogeography and the stepwise evolutionary colonization of intertidal habitat in the Liparocephalini are discussed. Based on the biogeographical analyses, we hypothesize that the ancestor of the Liparocephalini occurred along the Panthallassan Ocean, the direct antecedent of the Pacific Ocean, followed by repeated dispersals to the Nearctic from the Palearctic. We also hypothesize that ancestors of the Liparocephalini appear to have arisen in the littoral zone of beaches and then colonized rocky reef areas in the low tidal zone later through high‐ to mid‐tide zones. © The Willi Hennig Society 2009.
Observations on the breeding behaviour of the Stripe‐breasted tit (Parus fasciiventer) in Bwindi Impenetrable National Park, Uganda
Authors: Yatuha Jane , Dranzoa Christine 
Published: October 2009

AbstractThe motivation of this study was to investigate some hitherto unknown information on the breeding ecology of the Stripe‐breasted Tit (Parus fasciiventer) in Bwindi Impenetrable National Park, south‐western Uganda. Parus fasciiventer is one of the least studied and endemic bird species restricted to the montane forests of the Albertine Rift. Regionally, it is classified as near‐threatened. The study was carried out around the Institute of Tropical Forest Conservation Ruhija camp and the period of study was from January to June 2003. Data were generated through direct observation at the nest box sites of three active nests. Each of the nest boxes was monitored from the time of nest building to the time the chicks fledged. Results and comparative assessments from this study demonstrate that P. fasciiventer, compared with its temperate congeners like Great Tits (Parus major), Marsh Tits (Parus palustris), Crested Tits (Parus cristatus), Coal Tits (Parus ater) and Blue Tits (Parus caeruleus), raised small broods and had longer nestling period. The findings further revealed that the species is capable of raising more than one brood in a single breeding season and provide further evidence that it is a cooperative breeder. Parents participated equally in raising the young, an indication of pure parenting in the species.
Pelvic floor disorders and quality of life in women with self‐reported irritable bowel syndrome
Authors: WANG J. , VARMA M. G. , CREASMAN J. M. , SUBAK L. L. , BROWN J. S. , THOM D. H. , Van Den EEDEN S. K. 
Published: October 2009

Aliment Pharmacol Ther 31, 424–431SummaryBackground  Quality of life among women with irritable bowel syndrome may be affected by pelvic floor disorders.Aim  To assess the association of self‐reported irritable bowel syndrome with urinary incontinence, pelvic organ prolapse, sexual function and quality of life.Methods  We analysed data from the Reproductive Risks for Incontinence Study at Kaiser Permanente, a random population‐based study of 2109 racially diverse women (mean age = 56). Multivariate analyses assessed the association of irritable bowel syndrome with pelvic floor disorders and quality of life.Results  The prevalence of irritable bowel syndrome was 9.7% (n = 204). Women with irritable bowel had higher adjusted odds of reporting symptomatic pelvic organ prolapse (OR 2.4; 95% CI, 1.4–4.1) and urinary urgency (OR 1.4; 95% CI, 1.0–1.9); greater bother from pelvic organ prolapse (OR 4.3; 95% CI, 1.5–11.9) and faecal incontinence (OR 2.0; 95% CI, 1.3–3.2); greater lifestyle impact from urinary incontinence (OR 2.2; 95% CI, 1.3–3.8); and worse quality of life (P < 0.01). Women with irritable bowel reported more inability to relax and enjoy sexual activity (OR 1.8; 95% CI, 1.3–2.6) and lower ratings for sexual satisfaction (OR 1.8; 95% CI, 1.3–2.5), but no difference in sexual frequency, interest or ability to have an orgasm.Conclusions  Women with irritable bowel are more likely to report symptomatic pelvic organ prolapse and sexual dysfunction, and report lower quality of life.
Symptoms and quality of life in obese children and adolescents with non‐alcoholic fatty liver disease
Authors: KISTLER K. D. , MOLLESTON J. , UNALP A. , ABRAMS S. H. , BEHLING C. , SCHWIMMER J. B. ,   for the Nonalcoholic Steatohepatitis Clinical Research Network (NASH CRN)
Published: October 2009

Aliment Pharmacol Ther 31, 396–406SummaryBackground  Data on the quality of life (QOL) of children with non‐alcoholic fatty liver disease (NAFLD) are needed to estimate the true burden of illness in children with NAFLD.Aim  To characterize QOL and symptoms of children with NAFLD and to compare QOL in children with NAFLD with that in a sample of healthy children.Methods  Quality of life and symptoms were assessed in children with biopsy‐proven NAFLD enrolled in the NASH Clinical Research Network. PedsQL scores were compared with scores from healthy children. For children with NAFLD, between‐group comparisons were made to test associations of demography, histological severity, symptoms and QOL.Results  A total of 239 children (mean age 12.6 years) were studied. Children with NAFLD had worse total (72.8 vs. 83.8, P < 0.01), physical (77.2 vs. 87.5, P < 0.01) and psychosocial health (70.4 vs. 81.9, P < 0.01) scores compared with healthy children. QOL scores did not significantly differ by histological severity of NAFLD. Fatigue, trouble sleeping and sadness accounted for almost half of the variance in QOL scores. Impaired QOL was present in 39% of children with NAFLD.Conclusions  Children with NAFLD have a decrement in QOL. Symptoms were a major determinant of this impairment. Interventions are needed to restore and optimize QOL in children with NAFLD.
Informed consent document improvement does not increase patients' comprehension in biomedical research
Authors: Paris Adeline , Brandt Christian , Cornu Catherine , Maison Patrick , Thalamas Claire , Cracowski Jean‐Luc 
Published: October 2009

WHAT IS ALREADY KNOWN ABOUT THIS SUBJECT • Before enrolment, an informed consent (IC) document must be given to all participants by the investigator.• Most IC documents are long, contain much information and are difficult to understand.• Some methods to improve comprehension were tested, but they had limited effects. WHAT THIS STUDY ADDS • We failed to show that improving IC document comprehension through a lexicosyntactic approach or by a working group leads to better comprehension in our patient population, whichever method was used.• We confirm too that a study in real conditions is necessary.AIMS International guidelines on ethics in biomedical research require that the informed consent of all enrolled participants is obtained. A written document describing the research, the informed consent (IC) document, must be given to all participants by the investigator. Most IC documents are long, containing much information. The aim of the present study was to determine whether the modification of the IC document by a working group or systematic improvement in its lexicosyntactic readability can improve comprehension of the written information given to patients participating in biomedical research.METHODS One hundred and fifty‐nine patients were randomized to read one of the three versions of the IC document: unchanged document, document modified using systematic improvement of lexicosyntactic readability and document modified by a working group.RESULTS Neither the improvement in the lexicosyntactic readability, nor the intervention of the working group significantly improved the score of objective comprehension for the subjects included in this study: it was 66.6 (95% confidence interval 64.0, 69.2) for the control group, 68.8 (66.2, 71.4) for the group with the document improved for lexicosyntactic readability and 69.2 (66.0, 72.4) for the group who read the document improved by the working group (P= 0.38).CONCLUSIONS We failed to show that improving IC document comprehension through a lexicosyntactic approach or by a working group leads to better comprehension.
Pharmacokinetic interactions between ritonavir and quinine in healthy volunteers following concurrent administration
Authors: Soyinka Julius O. , Onyeji Cyprian O. , Omoruyi Sharon I. , Owolabi Adegbenga R. , Sarma Pullela V. , Cook James M. 
Published: October 2009

WHAT IS ALREADY KNOWN ABOUT THIS SUBJECT• Malaria is widespread across some areas of the world, most of which also bear the brunt of the human immunodeficiency virus (HIV) pandemic, resulting in a high incidence of co‐infection of both diseases.• Ritonavir, a HIV protease inhibitor, and quinine, an antimalarial agent effective against multidrug‐resistantPlasmodium falciparum, are likely to be administered concurrently for treatment of patients with HIV and malaria.• Both drugs are metabolized to a significant extent by CYP3A4 and ritonavir is a potent inhibitor of this enzyme.WHAT THIS STUDY ADDS• With increasing access to antiretroviral drugs, it is important that potential interactions between therapies for HIV and malaria infections are investigated.• In this study, concurrent administration of ritonavir with quinine was found to be associated with marked elevation in the plasma levels of the antimalarial and a pronounced decrease in plasma concentrations of 3‐hydroxyquinine, the major metabolite of quinine.• There was also a modest but significant increase (P< 0.05) in plasma concentrations of ritonavir in the presence of quinine.AIMSTo evaluate the pharmacokinetic interactions between ritonavir and quinine in healthy volunteers.METHODSTen healthy volunteers were each given 600‐mg single oral doses of quinine alone, ritonavir alone (200 mg every 12 h for 9 days), and quinine in combination with ritonavir, in a three‐period pharmacokinetic nonrandomized sequential design study. Quinine was co‐administered with the 15th dose of ritonavir. Blood samples collected at predetermined time intervals were analysed for ritonavir, quinine and its major metabolite, 3‐hydroxyquinine, using a validated high‐performance liquid chromatography method.RESULTSConcurrent ritonavir administration resulted in about fourfold increases in both theCmaxand AUCT[Cmax2.79 ± 0.22vs.10.72 ± 0.32 mg l−1, 95% confidence interval (CI) 7.81, 8.04; AUC 50.06 ± 2.52vs.220.47 ± 6.68 mg h−1 l−1, 95% CI 166.3, 175.3], a significant increase (P< 0.01) in the elimination half‐life (11.15 ± 0.80vs.13.37 ± 0.33 h, 95% CI 1.64, 2.77) and about a 4.5‐fold decrease in CL/F(12.01 ± 0.61vs.2.71 ± 0.09 l h−1) of quinine. Also, with ritonavir, there was a pronounced reduction of AUC(metabolite)/AUC(unchanged drug) ratio of quinine (1.35 ± 0.10vs.0.13 ± 0.02) along with a marked decrease inCmax(1.80 ± 0.12vs.0.96 ± 0.09 mg l−1) and AUC0–48h(62.80 ± 6.30vs.25.61 ± 2.44 mg h−1 l−1) of the metabolite. Similarly, quinine caused modest but significant increases (P< 0.01) in theCmax, AUC and eliminationT½of ritonavir.CONCLUSIONSDownward dosage adjustment of quinine appears necessary when concurrently administered with ritonavir.
Potential genetic risk factors in angiotensin‐converting enzyme‐inhibitor‐induced angio‐oedema
Authors: Bas Murat , Hoffmann Thomas K. , Tiemann Bernd , Dao Vu Thao‐Vi , Bantis Christos , Balz Vera , Schultz‐Coulon Hans‐Jürgen , Stark Thomas , Schuler Patrick , Greve Jens , Ivens Katrin , Bier Henning , Kojda Georg 
Published: October 2009

WHAT IS ALREADY KNOWN ABOUT THIS SUBJECT • Angiotensin‐converting enzyme inhibitor (ACEi)‐induced angio‐oedema is an underestimated clinical life‐threatening problem.• The incidence of this non‐allergic, bradykinin‐induced drug side‐effect is 1 : 4000.• Although most ACEi‐treated patients probably have an increased bradykinin plasma concentration, only 0.5% of them develop an angio‐oedema and nothing is known about potential risk factors. WHAT THIS STUDY ADDS • In our attempt to elucidate the unpredictable character of ACEi‐induced angio‐oedema, we investigated bradykinin B2 receptor 2/3 and c.C181T polymorphisms as well as the ACE insertion/deletion polymorphism in combination with serum ACE activity in 65 patients.• ACE insertion/deletion and bradykinin B2 receptor polymorphisms are not involved in the development of ACEi‐induced angio‐oedema.• Further studies should be carried out to clarify whether a combination of these polymorphisms might be a risk factor for ACEi‐induced angio‐oedema.AIMSThe pathophysiology of angiotensin‐converting enzyme inhibitor (ACEi)‐induced angio‐oedema remains unclear. We have investigated the impact of ACE insertion/deletion (I/D) polymorphism in combination with serum ACE activity as well as the bradykinin B2 receptor 2/3 and c.C181T polymorphisms.METHODSWe analysed the ACE I/D as well as bradykinin B2 (2/3 and C181T) receptor polymorphisms in 65 patients with documented episodes of ACEi‐induced angio‐oedema and 65 patients matched for age and sex being under ACEi treatment without history of angio‐oedema. Furthermore, we determined serum ACE activity in 47 of the 65 angio‐oedema patients 3 months after the angio‐oedema attack and compared these values with 51 healthy individuals (control II).RESULTSNo risk association was identified between ACE I/D (I‐allele: 0.42 vs. 0.41, D‐allele: 0.58 vs. 0.59; P= 0.095) or bradykinin B2 receptor polymorphisms and the development of angio‐oedema during ACEi treatment. We found a trend of lower serum ACE activity in ACE I/I genotypes in comparison with control II (I/I: 28 ± 4.5 vs. 33 ± 1.8 U l−1; ID: 39 ± 3.3 vs. 41 ± 1 U l−1; DD: 56 ± 6.7 vs. 52 ± 1.8 U l−1; P= 0.9).CONCLUSIONSOur data suggest that polymorphism of ACE I/D and the bradykinin B2 receptor polymorphisms are not involved in the development of ACEi‐induced angio‐oedema when considered individually. Further studies should be carried out to clarify whether a combination of these polymorphisms might be a risk factor for ACEi‐induced angio‐oedema.